diff --git a/Makefile b/Makefile index 4140e21f7..01bf8d64d 100644 --- a/Makefile +++ b/Makefile @@ -124,7 +124,7 @@ gen-project: $(PYMODEL) -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL) mv $(DEST)/prefixmap/biolink_model.yaml $(DEST)/prefixmap/biolink-model-prefix-map.json mv $(PYMODEL)/biolink*.py $(PYMODEL)/model.py - $(RUN) gen-pydantic --meta NONE src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel_v2.py + $(RUN) gen-pydantic --meta None src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel_v2.py $(RUN) gen-owl --mergeimports --no-metaclasses --no-type-objects --add-root-classes --mixins-as-expressions src/biolink_model/schema/biolink_model.yaml > $(DEST)/owl/biolink_model.owl.ttl cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml $(MAKE) id-prefixes diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql index de01934c3..6fd4805f5 100644 --- a/project/graphql/biolink_model.graphql +++ b/project/graphql/biolink_model.graphql @@ -1,3 +1,5 @@ +# metamodel_version: 1.7.0 +# version: 4.2.4 type AccessibleDnaRegion implements GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass { id: String! diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld index 4a360a598..11ddb9113 100644 --- a/project/jsonld/biolink_model.context.jsonld +++ b/project/jsonld/biolink_model.context.jsonld @@ -1,10 +1,11 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-10-10T17:38:44", + "generation_date": "2024-10-10T16:29:55", "source": "biolink_model.yaml" }, "@context": { + "xsd": "http://www.w3.org/2001/XMLSchema#", "AGRKB": "https://www.alliancegenome.org/", "APO": { "@id": "http://purl.obolibrary.org/obo/APO_", @@ -578,7 +579,6 @@ "@id": "http://www.w3.org/2003/01/geo/wgs84_pos", "@prefix": true }, - "xsd": "http://www.w3.org/2001/XMLSchema#", "@vocab": "https://w3id.org/biolink/vocab/", "active_in": { "@type": "@id", @@ -644,12 +644,11 @@ "@id": "affects_response_to" }, "affiliation": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "affiliation" }, "agent_type": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -733,7 +732,6 @@ }, "available_from": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -790,12 +788,11 @@ "@id": "catalyzes" }, "category": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "category" }, "causal_mechanism_qualifier": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -829,7 +826,6 @@ }, "clinical_approval_status": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1026,7 +1022,6 @@ }, "drug_regulatory_status_world_wide": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1092,7 +1087,6 @@ }, "FDA_adverse_event_level": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1146,7 +1140,6 @@ }, "genome_build": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1469,7 +1462,6 @@ }, "highest_FDA_approval_status": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1643,7 +1635,6 @@ }, "knowledge_level": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1702,7 +1693,6 @@ }, "logical_interpretation": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1722,7 +1712,6 @@ }, "max_research_phase": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1749,7 +1738,7 @@ "@id": "mentions" }, "mesh_terms": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "mesh_terms" }, "missing_from": { @@ -1830,7 +1819,6 @@ }, "object_direction_qualifier": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -1877,7 +1865,7 @@ "@id": "original_object" }, "original_predicate": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "original_predicate" }, "original_subject": { @@ -1915,7 +1903,6 @@ }, "phase": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2003,7 +1990,7 @@ "@id": "publications" }, "published_in": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "published_in" }, "publisher": { @@ -2030,7 +2017,6 @@ }, "reaction_direction": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2039,7 +2025,6 @@ }, "reaction_side": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2094,12 +2079,11 @@ "@id": "resistance_associated_with" }, "resource_id": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "resource_id" }, "resource_role": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2131,7 +2115,6 @@ }, "routes_of_delivery": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2204,7 +2187,6 @@ }, "strand": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2245,7 +2227,6 @@ }, "subject_direction_qualifier": { "@context": { - "@vocab": "@null", "text": "skos:notation", "description": "skos:prefLabel", "meaning": "@id" @@ -2296,7 +2277,7 @@ "@id": "supporting_document_year" }, "supporting_documents": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "supporting_documents" }, "supporting_study_cohort": { @@ -2312,11 +2293,11 @@ "@id": "supporting_study_metadata" }, "supporting_study_method_description": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "supporting_study_method_description" }, "supporting_study_method_type": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "supporting_study_method_type" }, "supporting_study_size": { @@ -2421,7 +2402,7 @@ "@id": "update_date" }, "upstream_resource_ids": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "upstream_resource_ids" }, "url": { @@ -2446,7 +2427,7 @@ "@id": "xenologous_to" }, "xref": { - "@type": "@id", + "@type": "xsd:anyURI", "@id": "xref" }, "AccessibleDnaRegion": { diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld index 86421c367..9eb772edc 100644 --- a/project/jsonld/biolink_model.jsonld +++ b/project/jsonld/biolink_model.jsonld @@ -2058,12 +2058,12 @@ ], "domain": "Entity", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", - "multivalued": true, "owner": "Entity", "domain_of": [ "Entity" ], "range": "Attribute", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2123,13 +2123,13 @@ ], "domain": "Attribute", "slot_uri": "https://w3id.org/biolink/vocab/has_quantitative_value", - "multivalued": true, "owner": "ChemicalExposure", "domain_of": [ "Attribute", "ChemicalExposure" ], "range": "QuantityValue", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -2271,12 +2271,12 @@ ], "domain": "Entity", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "multivalued": true, "owner": "Entity", "domain_of": [ "Entity" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2290,7 +2290,6 @@ "is_a": "type", "domain": "Entity", "slot_uri": "https://w3id.org/biolink/vocab/category", - "multivalued": true, "designates_type": true, "owner": "Entity", "domain_of": [ @@ -2298,6 +2297,7 @@ ], "is_class_field": true, "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2316,12 +2316,12 @@ "WIKIDATA" ], "slot_uri": "http://purl.org/dc/terms/type", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2461,13 +2461,13 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/synonym", - "multivalued": true, "owner": "GeneProductMixin", "domain_of": [ "NamedThing", "GeneProductMixin" ], "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2480,9 +2480,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/exact_synonym", - "multivalued": true, "owner": "exact_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2495,9 +2495,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/broad_synonym", - "multivalued": true, "owner": "broad_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2510,9 +2510,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/narrow_synonym", - "multivalued": true, "owner": "narrow_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2525,9 +2525,9 @@ "is_a": "synonym", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_synonym", - "multivalued": true, "owner": "related_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2586,7 +2586,6 @@ ], "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/xref", - "multivalued": true, "owner": "GeneProductMixin", "domain_of": [ "NamedThing", @@ -2596,6 +2595,7 @@ "GeneProductMixin" ], "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2636,9 +2636,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/support_graphs", - "multivalued": true, "owner": "support_graphs", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2686,12 +2686,12 @@ ], "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/retrieval_source_ids", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "RetrievalSource", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2764,9 +2764,9 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "http://purl.obolibrary.org/obo/go#systematic_synonym", - "multivalued": true, "owner": "systematic_synonym", "range": "label_type", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -2777,12 +2777,12 @@ "is_a": "node_property", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/affiliation", - "multivalued": true, "owner": "Agent", "domain_of": [ "Agent" ], "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3272,12 +3272,12 @@ "is_a": "node_property", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/authors", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3348,12 +3348,12 @@ "is_a": "node_property", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/pages", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3386,12 +3386,12 @@ "is_a": "node_property", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/keywords", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3408,12 +3408,12 @@ ], "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/mesh_terms", - "multivalued": true, "owner": "Publication", "domain_of": [ "Publication" ], "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3440,12 +3440,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_gene_or_gene_product", - "multivalued": true, "owner": "GeneGroupingMixin", "domain_of": [ "GeneGroupingMixin" ], "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3456,12 +3456,12 @@ "is_a": "has_gene_or_gene_product", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_gene", - "multivalued": true, "owner": "SequenceVariant", "domain_of": [ "SequenceVariant" ], "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3519,9 +3519,9 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_constituent", - "multivalued": true, "owner": "has_constituent", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3532,12 +3532,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_drug", - "multivalued": true, "owner": "Treatment", "domain_of": [ "Treatment" ], "range": "Drug", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3548,12 +3548,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_device", - "multivalued": true, "owner": "Treatment", "domain_of": [ "Treatment" ], "range": "Device", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3564,12 +3564,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_procedure", - "multivalued": true, "owner": "Treatment", "domain_of": [ "Treatment" ], "range": "Procedure", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3706,12 +3706,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/available_from", - "multivalued": true, "owner": "ChemicalEntity", "domain_of": [ "ChemicalEntity" ], "range": "DrugAvailabilityEnum", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3743,13 +3743,13 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_chemical_role", - "multivalued": true, "inherited": true, "owner": "ChemicalEntity", "domain_of": [ "ChemicalEntity" ], "range": "ChemicalRole", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3775,9 +3775,9 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/animal_model_available_from", - "multivalued": true, "owner": "animal_model_available_from", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -3856,12 +3856,12 @@ "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/routes_of_delivery", - "multivalued": true, "owner": "ChemicalMixture", "domain_of": [ "ChemicalMixture" ], "range": "DrugDeliveryEnum", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4054,12 +4054,12 @@ "description": "A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/predicate_mappings", - "multivalued": true, "owner": "MappingCollection", "domain_of": [ "MappingCollection" ], "range": "PredicateMapping", + "multivalued": true, "inlined": true, "inlined_as_list": true, "@type": "SlotDefinition" @@ -4070,8 +4070,8 @@ "description": "A list of terms from different schemas or terminology systems that have an identical meaning. Such terms often describe the same concept from different ontological perspectives.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/exact_matches", - "multivalued": true, "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4080,8 +4080,8 @@ "description": "A list of terms from different schemas or terminology systems that have a narrower meaning. Such terms often describe a more specific concept from different ontological perspectives.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/narrow_matches", - "multivalued": true, "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4090,8 +4090,8 @@ "description": "A list of terms from different schemas or terminology systems that have a broader meaning. Such terms often describe a more general concept from different ontological perspectives.", "from_schema": "https://w3id.org/biolink/biolink-model", "slot_uri": "https://w3id.org/biolink/vocab/broad_matches", - "multivalued": true, "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4590,12 +4590,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/qualifiers", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4727,12 +4727,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/catalyst_qualifier", - "multivalued": true, "owner": "ChemicalToChemicalDerivationAssociation", "domain_of": [ "ChemicalToChemicalDerivationAssociation" ], "range": "MacromolecularMachineMixin", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -4891,11 +4891,11 @@ ], "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_to", - "multivalued": true, "inherited": true, "owner": "related_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4913,11 +4913,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_to_at_concept_level", - "multivalued": true, "inherited": true, "owner": "related_to_at_concept_level", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4935,11 +4935,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_to_at_instance_level", - "multivalued": true, "inherited": true, "owner": "related_to_at_instance_level", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4961,11 +4961,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with", - "multivalued": true, "inherited": true, "owner": "associated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -4995,11 +4995,11 @@ "is_a": "related_to_at_concept_level", "domain": "OntologyClass", "slot_uri": "https://w3id.org/biolink/vocab/superclass_of", - "multivalued": true, "inherited": true, "owner": "superclass_of", "inverse": "subclass_of", "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5053,11 +5053,11 @@ "is_a": "related_to_at_concept_level", "domain": "OntologyClass", "slot_uri": "https://w3id.org/biolink/vocab/subclass_of", - "multivalued": true, "inherited": true, "owner": "subclass_of", "inverse": "superclass_of", "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5091,11 +5091,11 @@ "is_a": "exact_match", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/same_as", - "multivalued": true, "inherited": true, "owner": "same_as", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5128,11 +5128,11 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/close_match", - "multivalued": true, "inherited": true, "owner": "close_match", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5158,7 +5158,6 @@ "is_a": "close_match", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/exact_match", - "multivalued": true, "inherited": true, "owner": "PredicateMapping", "domain_of": [ @@ -5166,6 +5165,7 @@ ], "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5195,7 +5195,6 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/broad_match", - "multivalued": true, "inherited": true, "owner": "PredicateMapping", "domain_of": [ @@ -5203,6 +5202,7 @@ ], "inverse": "narrow_match", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5227,7 +5227,6 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/narrow_match", - "multivalued": true, "inherited": true, "owner": "PredicateMapping", "domain_of": [ @@ -5235,6 +5234,7 @@ ], "inverse": "broad_match", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5254,11 +5254,11 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/member_of", - "multivalued": true, "inherited": true, "owner": "member_of", "inverse": "has_member", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5276,11 +5276,11 @@ "is_a": "related_to_at_concept_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_member", - "multivalued": true, "inherited": true, "owner": "has_member", "inverse": "member_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5305,11 +5305,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/opposite_of", - "multivalued": true, "inherited": true, "owner": "opposite_of", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5333,11 +5333,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/affects_likelihood_of", - "multivalued": true, "inherited": true, "owner": "affects_likelihood_of", "inverse": "likelihood_affected_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5347,11 +5347,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/likelihood_affected_by", - "multivalued": true, "inherited": true, "owner": "likelihood_affected_by", "inverse": "affects_likelihood_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5369,11 +5369,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_likelihood_of", - "multivalued": true, "inherited": true, "owner": "associated_with_likelihood_of", "inverse": "likelihood_associated_with", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5384,11 +5384,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/likelihood_associated_with", - "multivalued": true, "inherited": true, "owner": "likelihood_associated_with", "inverse": "associated_with_likelihood_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5406,11 +5406,11 @@ "is_a": "associated_with_likelihood_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_increased_likelihood_of", - "multivalued": true, "inherited": true, "owner": "associated_with_increased_likelihood_of", "inverse": "increased_likelihood_associated_with", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5421,11 +5421,11 @@ "is_a": "likelihood_associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/increased_likelihood_associated_with", - "multivalued": true, "inherited": true, "owner": "increased_likelihood_associated_with", "inverse": "associated_with_increased_likelihood_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5443,11 +5443,11 @@ "is_a": "associated_with_likelihood_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_decreased_likelihood_of", - "multivalued": true, "inherited": true, "owner": "associated_with_decreased_likelihood_of", "inverse": "decreased_likelihood_associated_with", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5458,11 +5458,11 @@ "is_a": "likelihood_associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/decreased_likelihood_associated_with", - "multivalued": true, "inherited": true, "owner": "decreased_likelihood_associated_with", "inverse": "associated_with_decreased_likelihood_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5480,11 +5480,11 @@ "is_a": "related_to_at_instance_level", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/target_for", - "multivalued": true, "inherited": true, "owner": "target_for", "inverse": "has_target", "range": "Disease", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5494,11 +5494,11 @@ "is_a": "related_to_at_instance_level", "domain": "Disease", "slot_uri": "https://w3id.org/biolink/vocab/has_target", - "multivalued": true, "inherited": true, "owner": "has_target", "inverse": "target_for", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5518,11 +5518,11 @@ "is_a": "related_to_at_instance_level", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/active_in", - "multivalued": true, "inherited": true, "owner": "active_in", "inverse": "has_active_component", "range": "CellularComponent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5532,11 +5532,11 @@ "is_a": "related_to_at_instance_level", "domain": "CellularComponent", "slot_uri": "https://w3id.org/biolink/vocab/has_active_component", - "multivalued": true, "inherited": true, "owner": "has_active_component", "inverse": "active_in", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5557,11 +5557,11 @@ "is_a": "related_to_at_instance_level", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of", "inverse": "has_upstream_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5571,11 +5571,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_upstream_actor", - "multivalued": true, "inherited": true, "owner": "has_upstream_actor", "inverse": "acts_upstream_of", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5596,11 +5596,11 @@ "is_a": "acts_upstream_of", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_positive_effect", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_positive_effect", "inverse": "has_positive_upstream_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5610,11 +5610,11 @@ "is_a": "has_upstream_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_positive_upstream_actor", - "multivalued": true, "inherited": true, "owner": "has_positive_upstream_actor", "inverse": "acts_upstream_of_positive_effect", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5635,11 +5635,11 @@ "is_a": "acts_upstream_of", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_negative_effect", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_negative_effect", "inverse": "has_negative_upstream_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5649,11 +5649,11 @@ "is_a": "has_upstream_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_negative_upstream_actor", - "multivalued": true, "inherited": true, "owner": "has_negative_upstream_actor", "inverse": "acts_upstream_of_negative_effect", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5674,11 +5674,11 @@ "is_a": "acts_upstream_of", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_or_within", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_or_within", "inverse": "has_upstream_or_within_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5688,11 +5688,11 @@ "is_a": "has_upstream_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_upstream_or_within_actor", - "multivalued": true, "inherited": true, "owner": "has_upstream_or_within_actor", "inverse": "acts_upstream_of_or_within", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5713,11 +5713,11 @@ "is_a": "acts_upstream_of_or_within", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_or_within_positive_effect", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_or_within_positive_effect", "inverse": "has_positive_upstream_or_within_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5727,11 +5727,11 @@ "is_a": "has_upstream_or_within_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_positive_upstream_or_within_actor", - "multivalued": true, "inherited": true, "owner": "has_positive_upstream_or_within_actor", "inverse": "acts_upstream_of_or_within_positive_effect", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5752,11 +5752,11 @@ "is_a": "acts_upstream_of_or_within", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/acts_upstream_of_or_within_negative_effect", - "multivalued": true, "inherited": true, "owner": "acts_upstream_of_or_within_negative_effect", "inverse": "has_negative_upstream_or_within_actor", "range": "BiologicalProcess", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5766,11 +5766,11 @@ "is_a": "has_upstream_or_within_actor", "domain": "BiologicalProcess", "slot_uri": "https://w3id.org/biolink/vocab/has_negative_upstream_or_within_actor", - "multivalued": true, "inherited": true, "owner": "has_negative_upstream_or_within_actor", "inverse": "acts_upstream_of_or_within_negative_effect", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -5788,11 +5788,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/mentions", - "multivalued": true, "inherited": true, "owner": "mentions", "inverse": "mentioned_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5803,11 +5803,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/mentioned_by", - "multivalued": true, "inherited": true, "owner": "mentioned_by", "inverse": "mentions", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5824,11 +5824,11 @@ "abstract": true, "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/contributor", - "multivalued": true, "inherited": true, "owner": "contributor", "inverse": "has_contributor", "range": "InformationContentEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5838,11 +5838,11 @@ "is_a": "related_to_at_instance_level", "domain": "InformationContentEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_contributor", - "multivalued": true, "inherited": true, "owner": "has_contributor", "inverse": "contributor", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5853,11 +5853,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/provider", - "multivalued": true, "inherited": true, "owner": "provider", "inverse": "has_provider", "range": "InformationContentEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5867,11 +5867,11 @@ "is_a": "has_contributor", "domain": "InformationContentEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_provider", - "multivalued": true, "inherited": true, "owner": "has_provider", "inverse": "provider", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5886,11 +5886,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/publisher", - "multivalued": true, "inherited": true, "owner": "publisher", "inverse": "has_publisher", "range": "Publication", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5900,11 +5900,11 @@ "is_a": "has_contributor", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/has_publisher", - "multivalued": true, "inherited": true, "owner": "has_publisher", "inverse": "publisher", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5918,11 +5918,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/editor", - "multivalued": true, "inherited": true, "owner": "editor", "inverse": "has_editor", "range": "Publication", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5932,11 +5932,11 @@ "is_a": "has_contributor", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/has_editor", - "multivalued": true, "inherited": true, "owner": "has_editor", "inverse": "editor", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5951,11 +5951,11 @@ "is_a": "contributor", "domain": "Agent", "slot_uri": "https://w3id.org/biolink/vocab/author", - "multivalued": true, "inherited": true, "owner": "author", "inverse": "has_author", "range": "Publication", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5965,11 +5965,11 @@ "is_a": "has_contributor", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/has_author", - "multivalued": true, "inherited": true, "owner": "has_author", "inverse": "author", "range": "Agent", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -5990,11 +5990,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/assesses", - "multivalued": true, "inherited": true, "owner": "assesses", "inverse": "is_assessed_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6004,11 +6004,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/is_assessed_by", - "multivalued": true, "inherited": true, "owner": "is_assessed_by", "inverse": "assesses", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6029,11 +6029,11 @@ "mixin": true, "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/interacts_with", - "multivalued": true, "inherited": true, "owner": "interacts_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6075,11 +6075,11 @@ ], "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/physically_interacts_with", - "multivalued": true, "inherited": true, "owner": "physically_interacts_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6110,11 +6110,11 @@ "is_a": "physically_interacts_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/directly_physically_interacts_with", - "multivalued": true, "inherited": true, "owner": "directly_physically_interacts_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6136,11 +6136,11 @@ "is_a": "directly_physically_interacts_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/binds", - "multivalued": true, "inherited": true, "owner": "binds", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6157,11 +6157,11 @@ "is_a": "physically_interacts_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/indirectly_physically_interacts_with", - "multivalued": true, "inherited": true, "owner": "indirectly_physically_interacts_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6185,11 +6185,11 @@ "is_a": "interacts_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/genetically_interacts_with", - "multivalued": true, "inherited": true, "owner": "genetically_interacts_with", "symmetric": true, "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6210,11 +6210,11 @@ "is_a": "genetically_interacts_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/gene_fusion_with", - "multivalued": true, "inherited": true, "owner": "gene_fusion_with", "symmetric": true, "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6235,11 +6235,11 @@ "is_a": "genetically_interacts_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/genetic_neighborhood_of", - "multivalued": true, "inherited": true, "owner": "genetic_neighborhood_of", "symmetric": true, "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6302,11 +6302,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/affects", - "multivalued": true, "inherited": true, "owner": "affects", "inverse": "affected_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6317,11 +6317,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/affected_by", - "multivalued": true, "inherited": true, "owner": "affected_by", "inverse": "affects", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6345,11 +6345,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_sensitivity_to", - "multivalued": true, "inherited": true, "owner": "associated_with_sensitivity_to", "inverse": "sensitivity_associated_with", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6359,11 +6359,11 @@ "is_a": "associated_with", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/sensitivity_associated_with", - "multivalued": true, "inherited": true, "owner": "sensitivity_associated_with", "inverse": "associated_with_sensitivity_to", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6381,11 +6381,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/associated_with_resistance_to", - "multivalued": true, "inherited": true, "owner": "associated_with_resistance_to", "inverse": "resistance_associated_with", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6395,11 +6395,11 @@ "is_a": "associated_with", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/resistance_associated_with", - "multivalued": true, "inherited": true, "owner": "resistance_associated_with", "inverse": "associated_with_resistance_to", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6425,11 +6425,11 @@ "is_a": "related_to_at_instance_level", "domain": "DiagnosticAid", "slot_uri": "https://w3id.org/biolink/vocab/diagnoses", - "multivalued": true, "inherited": true, "owner": "diagnoses", "inverse": "is_diagnosed_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6439,11 +6439,11 @@ "is_a": "related_to_at_instance_level", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/is_diagnosed_by", - "multivalued": true, "inherited": true, "owner": "is_diagnosed_by", "inverse": "diagnoses", "range": "DiagnosticAid", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6456,11 +6456,11 @@ "mixin": true, "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/increases_amount_or_activity_of", - "multivalued": true, "inherited": true, "owner": "increases_amount_or_activity_of", "inverse": "amount_or_activity_increased_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6471,11 +6471,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/amount_or_activity_increased_by", - "multivalued": true, "inherited": true, "owner": "amount_or_activity_increased_by", "inverse": "increases_amount_or_activity_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6488,11 +6488,11 @@ "mixin": true, "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/decreases_amount_or_activity_of", - "multivalued": true, "inherited": true, "owner": "decreases_amount_or_activity_of", "inverse": "amount_or_activity_decreased_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6503,11 +6503,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/amount_or_activity_decreased_by", - "multivalued": true, "inherited": true, "owner": "amount_or_activity_decreased_by", "inverse": "decreases_amount_or_activity_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6556,11 +6556,11 @@ "is_a": "affects", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/affects_response_to", - "multivalued": true, "inherited": true, "owner": "affects_response_to", "inverse": "response_affected_by", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6575,11 +6575,11 @@ "is_a": "affected_by", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/response_affected_by", - "multivalued": true, "inherited": true, "owner": "response_affected_by", "inverse": "affects_response_to", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6609,11 +6609,11 @@ "is_a": "affects_response_to", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/increases_response_to", - "multivalued": true, "inherited": true, "owner": "increases_response_to", "inverse": "response_increased_by", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6627,11 +6627,11 @@ "is_a": "response_affected_by", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/response_increased_by", - "multivalued": true, "inherited": true, "owner": "response_increased_by", "inverse": "increases_response_to", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6664,11 +6664,11 @@ "is_a": "affects_response_to", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/decreases_response_to", - "multivalued": true, "inherited": true, "owner": "decreases_response_to", "inverse": "response_decreased_by", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6682,11 +6682,11 @@ "is_a": "response_affected_by", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/response_decreased_by", - "multivalued": true, "inherited": true, "owner": "response_decreased_by", "inverse": "decreases_response_to", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6721,11 +6721,11 @@ ], "domain": "PhysicalEssenceOrOccurrent", "slot_uri": "https://w3id.org/biolink/vocab/regulates", - "multivalued": true, "inherited": true, "owner": "regulates", "inverse": "regulated_by", "range": "PhysicalEssenceOrOccurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6736,11 +6736,11 @@ "is_a": "affected_by", "domain": "PhysicalEssenceOrOccurrent", "slot_uri": "https://w3id.org/biolink/vocab/regulated_by", - "multivalued": true, "inherited": true, "owner": "regulated_by", "inverse": "regulates", "range": "PhysicalEssenceOrOccurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6778,11 +6778,11 @@ "is_a": "affects", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disrupts", - "multivalued": true, "inherited": true, "owner": "disrupts", "inverse": "disrupted_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6793,11 +6793,11 @@ "is_a": "affected_by", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disrupted_by", - "multivalued": true, "inherited": true, "owner": "disrupted_by", "inverse": "disrupts", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6821,11 +6821,11 @@ "is_a": "related_to_at_instance_level", "domain": "GeneProductMixin", "slot_uri": "https://w3id.org/biolink/vocab/gene_product_of", - "multivalued": true, "inherited": true, "owner": "gene_product_of", "inverse": "has_gene_product", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6850,11 +6850,11 @@ "is_a": "related_to_at_instance_level", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/has_gene_product", - "multivalued": true, "inherited": true, "owner": "has_gene_product", "inverse": "gene_product_of", "range": "GeneProductMixin", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -6870,11 +6870,11 @@ "is_a": "related_to_at_instance_level", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/transcribed_to", - "multivalued": true, "inherited": true, "owner": "transcribed_to", "inverse": "transcribed_from", "range": "Transcript", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6896,11 +6896,11 @@ "is_a": "related_to_at_instance_level", "domain": "Transcript", "slot_uri": "https://w3id.org/biolink/vocab/transcribed_from", - "multivalued": true, "inherited": true, "owner": "transcribed_from", "inverse": "transcribed_to", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6922,11 +6922,11 @@ "is_a": "related_to_at_instance_level", "domain": "Transcript", "slot_uri": "https://w3id.org/biolink/vocab/translates_to", - "multivalued": true, "inherited": true, "owner": "translates_to", "inverse": "translation_of", "range": "Protein", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6941,11 +6941,11 @@ "is_a": "related_to_at_instance_level", "domain": "Protein", "slot_uri": "https://w3id.org/biolink/vocab/translation_of", - "multivalued": true, "inherited": true, "owner": "translation_of", "inverse": "translates_to", "range": "Transcript", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -6979,11 +6979,11 @@ "is_a": "similar_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/homologous_to", - "multivalued": true, "inherited": true, "owner": "homologous_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7007,11 +7007,11 @@ "is_a": "homologous_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/paralogous_to", - "multivalued": true, "inherited": true, "owner": "paralogous_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7036,11 +7036,11 @@ "is_a": "homologous_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/orthologous_to", - "multivalued": true, "inherited": true, "owner": "orthologous_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7064,11 +7064,11 @@ "is_a": "homologous_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/xenologous_to", - "multivalued": true, "inherited": true, "owner": "xenologous_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7260,11 +7260,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/coexists_with", - "multivalued": true, "inherited": true, "owner": "coexists_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7288,11 +7288,11 @@ "is_a": "coexists_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/in_pathway_with", - "multivalued": true, "inherited": true, "owner": "in_pathway_with", "symmetric": true, "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7320,11 +7320,11 @@ "is_a": "coexists_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/in_complex_with", - "multivalued": true, "inherited": true, "owner": "in_complex_with", "symmetric": true, "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7346,11 +7346,11 @@ "is_a": "coexists_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/in_cell_population_with", - "multivalued": true, "inherited": true, "owner": "in_cell_population_with", "symmetric": true, "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7375,11 +7375,11 @@ "is_a": "coexists_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/colocalizes_with", - "multivalued": true, "inherited": true, "owner": "colocalizes_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7391,11 +7391,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/genetic_association", - "multivalued": true, "inherited": true, "owner": "genetic_association", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7424,11 +7424,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/genetically_associated_with", - "multivalued": true, "inherited": true, "owner": "genetically_associated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7458,11 +7458,11 @@ "is_a": "genetically_associated_with", "domain": "Gene", "slot_uri": "https://w3id.org/biolink/vocab/gene_associated_with_condition", - "multivalued": true, "inherited": true, "owner": "gene_associated_with_condition", "inverse": "condition_associated_with_gene", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7483,11 +7483,11 @@ "is_a": "genetically_associated_with", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_associated_with_gene", - "multivalued": true, "inherited": true, "owner": "condition_associated_with_gene", "inverse": "gene_associated_with_condition", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7520,11 +7520,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/contributes_to", - "multivalued": true, "inherited": true, "owner": "contributes_to", "inverse": "contribution_from", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7537,11 +7537,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/contribution_from", - "multivalued": true, "inherited": true, "owner": "contribution_from", "inverse": "contributes_to", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7598,11 +7598,11 @@ "is_a": "contributes_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/causes", - "multivalued": true, "inherited": true, "owner": "causes", "inverse": "caused_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7633,11 +7633,11 @@ "is_a": "contribution_from", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/caused_by", - "multivalued": true, "inherited": true, "owner": "caused_by", "inverse": "causes", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7674,11 +7674,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/ameliorates_condition", - "multivalued": true, "inherited": true, "owner": "ameliorates_condition", "inverse": "condition_ameliorated_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7688,11 +7688,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_ameliorated_by", - "multivalued": true, "inherited": true, "owner": "condition_ameliorated_by", "inverse": "ameliorates_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7729,11 +7729,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/preventative_for_condition", - "multivalued": true, "inherited": true, "owner": "preventative_for_condition", "inverse": "condition_prevented_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7743,11 +7743,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_prevented_by", - "multivalued": true, "inherited": true, "owner": "condition_prevented_by", "inverse": "preventative_for_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7775,11 +7775,11 @@ "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/promotes_condition", - "multivalued": true, "inherited": true, "owner": "promotes_condition", "inverse": "condition_promoted_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7790,11 +7790,11 @@ "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_promoted_by", - "multivalued": true, "inherited": true, "owner": "condition_promoted_by", "inverse": "promotes_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7825,11 +7825,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/predisposes_to_condition", - "multivalued": true, "inherited": true, "owner": "predisposes_to_condition", "inverse": "condition_predisposed_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7839,11 +7839,11 @@ "is_a": "likelihood_affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_predisposed_by", - "multivalued": true, "inherited": true, "owner": "condition_predisposed_by", "inverse": "predisposes_to_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7880,11 +7880,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/exacerbates_condition", - "multivalued": true, "inherited": true, "owner": "exacerbates_condition", "inverse": "condition_exacerbated_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7897,11 +7897,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/condition_exacerbated_by", - "multivalued": true, "inherited": true, "owner": "condition_exacerbated_by", "inverse": "exacerbates_condition", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -7966,11 +7966,11 @@ "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/treats", - "multivalued": true, "inherited": true, "owner": "treats", "inverse": "treated_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -7991,11 +7991,11 @@ "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treated_by", - "multivalued": true, "inherited": true, "owner": "treated_by", "inverse": "treats", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8020,11 +8020,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/studied_to_treat", - "multivalued": true, "inherited": true, "owner": "studied_to_treat", "inverse": "treated_in_studies_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8051,11 +8051,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/in_clinical_trials_for", - "multivalued": true, "inherited": true, "owner": "in_clinical_trials_for", "inverse": "tested_by_clinical_trials_of", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8068,11 +8068,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/tested_by_clinical_trials_of", - "multivalued": true, "inherited": true, "owner": "tested_by_clinical_trials_of", "inverse": "in_clinical_trials_for", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8086,11 +8086,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treated_in_studies_by", - "multivalued": true, "inherited": true, "owner": "treated_in_studies_by", "inverse": "studied_to_treat", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8104,11 +8104,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/tested_by_preclinical_trials_of", - "multivalued": true, "inherited": true, "owner": "tested_by_preclinical_trials_of", "inverse": "in_preclinical_trials_for", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8133,11 +8133,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/in_preclinical_trials_for", - "multivalued": true, "inherited": true, "owner": "in_preclinical_trials_for", "inverse": "tested_by_preclinical_trials_of", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8164,11 +8164,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/beneficial_in_models_for", - "multivalued": true, "inherited": true, "owner": "beneficial_in_models_for", "inverse": "models_demonstrating_benefits_for", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8181,11 +8181,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/models_demonstrating_benefits_for", - "multivalued": true, "inherited": true, "owner": "models_demonstrating_benefits_for", "inverse": "beneficial_in_models_for", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8218,11 +8218,11 @@ ], "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/applied_to_treat", - "multivalued": true, "inherited": true, "owner": "applied_to_treat", "inverse": "treatment_applications_from", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8235,11 +8235,11 @@ ], "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/treatment_applications_from", - "multivalued": true, "inherited": true, "owner": "treatment_applications_from", "inverse": "applied_to_treat", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8268,11 +8268,11 @@ "mixin": true, "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/treats_or_applied_or_studied_to_treat", - "multivalued": true, "inherited": true, "owner": "treats_or_applied_or_studied_to_treat", "inverse": "subject_of_treatment_application_or_study_for_treatment_by", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8283,11 +8283,11 @@ "mixin": true, "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/subject_of_treatment_application_or_study_for_treatment_by", - "multivalued": true, "inherited": true, "owner": "subject_of_treatment_application_or_study_for_treatment_by", "inverse": "treats_or_applied_or_studied_to_treat", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8316,11 +8316,11 @@ "is_a": "associated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/correlated_with", - "multivalued": true, "inherited": true, "owner": "correlated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8349,11 +8349,11 @@ "is_a": "correlated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/positively_correlated_with", - "multivalued": true, "inherited": true, "owner": "positively_correlated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8382,11 +8382,11 @@ "is_a": "correlated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/negatively_correlated_with", - "multivalued": true, "inherited": true, "owner": "negatively_correlated_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8407,11 +8407,11 @@ "is_a": "correlated_with", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/occurs_together_in_literature_with", - "multivalued": true, "inherited": true, "owner": "occurs_together_in_literature_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8429,11 +8429,11 @@ "is_a": "correlated_with", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/coexpressed_with", - "multivalued": true, "inherited": true, "owner": "coexpressed_with", "symmetric": true, "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8452,11 +8452,11 @@ "is_a": "correlated_with", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/has_biomarker", - "multivalued": true, "inherited": true, "owner": "has_biomarker", "inverse": "biomarker_for", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8490,11 +8490,11 @@ "is_a": "correlated_with", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/biomarker_for", - "multivalued": true, "inherited": true, "owner": "biomarker_for", "inverse": "has_biomarker", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8522,11 +8522,11 @@ "is_a": "located_in", "domain": "GeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/expressed_in", - "multivalued": true, "inherited": true, "owner": "expressed_in", "inverse": "expresses", "range": "AnatomicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8546,11 +8546,11 @@ "is_a": "location_of", "domain": "AnatomicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/expresses", - "multivalued": true, "inherited": true, "owner": "expresses", "inverse": "expressed_in", "range": "GeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -8591,11 +8591,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_phenotype", - "multivalued": true, "inherited": true, "owner": "has_phenotype", "inverse": "phenotype_of", "range": "PhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8605,11 +8605,11 @@ "is_a": "related_to_at_instance_level", "domain": "PhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/phenotype_of", - "multivalued": true, "inherited": true, "owner": "phenotype_of", "inverse": "has_phenotype", "range": "BiologicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8652,11 +8652,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/occurs_in", - "multivalued": true, "inherited": true, "owner": "occurs_in", "inverse": "contains_process", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8666,11 +8666,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/contains_process", - "multivalued": true, "inherited": true, "owner": "contains_process", "inverse": "occurs_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8738,11 +8738,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/located_in", - "multivalued": true, "inherited": true, "owner": "located_in", "inverse": "location_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8769,11 +8769,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/location_of", - "multivalued": true, "inherited": true, "owner": "location_of", "inverse": "located_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8788,11 +8788,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disease_has_location", - "multivalued": true, "inherited": true, "owner": "disease_has_location", "inverse": "location_of_disease", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8802,11 +8802,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/location_of_disease", - "multivalued": true, "inherited": true, "owner": "location_of_disease", "inverse": "disease_has_location", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8831,11 +8831,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/similar_to", - "multivalued": true, "inherited": true, "owner": "similar_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8865,11 +8865,11 @@ "is_a": "similar_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/chemically_similar_to", - "multivalued": true, "inherited": true, "owner": "chemically_similar_to", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8890,11 +8890,11 @@ "is_a": "related_to_at_instance_level", "domain": "NucleicAcidEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_sequence_location", - "multivalued": true, "inherited": true, "owner": "has_sequence_location", "inverse": "sequence_location_of", "range": "NucleicAcidEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8904,11 +8904,11 @@ "is_a": "related_to_at_instance_level", "domain": "NucleicAcidEntity", "slot_uri": "https://w3id.org/biolink/vocab/sequence_location_of", - "multivalued": true, "inherited": true, "owner": "sequence_location_of", "inverse": "has_sequence_location", "range": "NucleicAcidEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8935,11 +8935,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/model_of", - "multivalued": true, "inherited": true, "owner": "model_of", "inverse": "models", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8949,11 +8949,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/models", - "multivalued": true, "inherited": true, "owner": "models", "inverse": "model_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -8984,11 +8984,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/overlaps", - "multivalued": true, "inherited": true, "owner": "overlaps", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9053,11 +9053,11 @@ "is_a": "overlaps", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_part", - "multivalued": true, "inherited": true, "owner": "has_part", "inverse": "part_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9081,11 +9081,11 @@ "is_a": "has_part", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_plasma_membrane_part", - "multivalued": true, "inherited": true, "owner": "has_plasma_membrane_part", "inverse": "plasma_membrane_part_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9109,11 +9109,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/composed_primarily_of", - "multivalued": true, "inherited": true, "owner": "composed_primarily_of", "inverse": "primarily_composed_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9123,11 +9123,11 @@ "is_a": "related_to", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/primarily_composed_of", - "multivalued": true, "inherited": true, "owner": "primarily_composed_of", "inverse": "composed_primarily_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9137,11 +9137,11 @@ "is_a": "part_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/plasma_membrane_part_of", - "multivalued": true, "inherited": true, "owner": "plasma_membrane_part_of", "inverse": "has_plasma_membrane_part", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9219,11 +9219,11 @@ "is_a": "overlaps", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/part_of", - "multivalued": true, "inherited": true, "owner": "part_of", "inverse": "has_part", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9268,7 +9268,6 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_input", - "multivalued": true, "inherited": true, "owner": "BiologicalProcessOrActivity", "domain_of": [ @@ -9276,6 +9275,7 @@ ], "inverse": "is_input_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9291,11 +9291,11 @@ "is_a": "participates_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/is_input_of", - "multivalued": true, "inherited": true, "owner": "is_input_of", "inverse": "has_input", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9335,7 +9335,6 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_output", - "multivalued": true, "inherited": true, "owner": "BiologicalProcessOrActivity", "domain_of": [ @@ -9343,6 +9342,7 @@ ], "inverse": "is_output_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9361,11 +9361,11 @@ "is_a": "participates_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/is_output_of", - "multivalued": true, "inherited": true, "owner": "is_output_of", "inverse": "has_output", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9414,11 +9414,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_participant", - "multivalued": true, "inherited": true, "owner": "has_participant", "inverse": "participates_in", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9439,11 +9439,11 @@ "is_a": "participates_in", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/catalyzes", - "multivalued": true, "inherited": true, "owner": "catalyzes", "inverse": "has_catalyst", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9453,11 +9453,11 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_catalyst", - "multivalued": true, "inherited": true, "owner": "has_catalyst", "inverse": "catalyzes", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9475,11 +9475,11 @@ "is_a": "has_participant", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/has_substrate", - "multivalued": true, "inherited": true, "owner": "has_substrate", "inverse": "is_substrate_of", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9490,11 +9490,11 @@ "is_a": "participates_in", "domain": "ChemicalEntityOrGeneOrGeneProduct", "slot_uri": "https://w3id.org/biolink/vocab/is_substrate_of", - "multivalued": true, "inherited": true, "owner": "is_substrate_of", "inverse": "has_substrate", "range": "ChemicalEntityOrGeneOrGeneProduct", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9527,11 +9527,11 @@ "is_a": "related_to_at_instance_level", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/participates_in", - "multivalued": true, "inherited": true, "owner": "participates_in", "inverse": "has_participant", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9565,11 +9565,11 @@ "is_a": "participates_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/actively_involved_in", - "multivalued": true, "inherited": true, "owner": "actively_involved_in", "inverse": "actively_involves", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9582,11 +9582,11 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/actively_involves", - "multivalued": true, "inherited": true, "owner": "actively_involves", "inverse": "actively_involved_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9614,11 +9614,11 @@ "is_a": "actively_involved_in", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/capable_of", - "multivalued": true, "inherited": true, "owner": "capable_of", "inverse": "can_be_carried_out_by", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -9629,11 +9629,11 @@ "is_a": "actively_involves", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/can_be_carried_out_by", - "multivalued": true, "inherited": true, "owner": "can_be_carried_out_by", "inverse": "capable_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9657,11 +9657,11 @@ "is_a": "participates_in", "domain": "PhysicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/enables", - "multivalued": true, "inherited": true, "owner": "enables", "inverse": "enabled_by", "range": "BiologicalProcessOrActivity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9685,7 +9685,6 @@ "is_a": "has_participant", "domain": "BiologicalProcessOrActivity", "slot_uri": "https://w3id.org/biolink/vocab/enabled_by", - "multivalued": true, "inherited": true, "owner": "BiologicalProcessOrActivity", "domain_of": [ @@ -9693,6 +9692,7 @@ ], "inverse": "enables", "range": "PhysicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9715,11 +9715,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/derives_into", - "multivalued": true, "inherited": true, "owner": "derives_into", "inverse": "derives_from", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9750,11 +9750,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/derives_from", - "multivalued": true, "inherited": true, "owner": "derives_from", "inverse": "derives_into", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9774,11 +9774,11 @@ "is_a": "derives_from", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/is_metabolite_of", - "multivalued": true, "inherited": true, "owner": "is_metabolite_of", "inverse": "has_metabolite", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9805,11 +9805,11 @@ "is_a": "derives_into", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_metabolite", - "multivalued": true, "inherited": true, "owner": "has_metabolite", "inverse": "is_metabolite_of", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9823,11 +9823,11 @@ "is_a": "part_of", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/food_component_of", - "multivalued": true, "inherited": true, "owner": "food_component_of", "inverse": "has_food_component", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9848,11 +9848,11 @@ "is_a": "has_part", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_food_component", - "multivalued": true, "inherited": true, "owner": "has_food_component", "inverse": "food_component_of", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9866,11 +9866,11 @@ "is_a": "food_component_of", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/nutrient_of", - "multivalued": true, "inherited": true, "owner": "nutrient_of", "inverse": "has_nutrient", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9894,11 +9894,11 @@ "is_a": "has_food_component", "domain": "ChemicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_nutrient", - "multivalued": true, "inherited": true, "owner": "has_nutrient", "inverse": "nutrient_of", "range": "ChemicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9915,11 +9915,11 @@ "is_a": "part_of", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/is_active_ingredient_of", - "multivalued": true, "inherited": true, "owner": "is_active_ingredient_of", "inverse": "has_active_ingredient", "range": "Drug", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9948,11 +9948,11 @@ "is_a": "has_part", "domain": "Drug", "slot_uri": "https://w3id.org/biolink/vocab/has_active_ingredient", - "multivalued": true, "inherited": true, "owner": "has_active_ingredient", "inverse": "is_active_ingredient_of", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9969,11 +9969,11 @@ "is_a": "part_of", "domain": "MolecularEntity", "slot_uri": "https://w3id.org/biolink/vocab/is_excipient_of", - "multivalued": true, "inherited": true, "owner": "is_excipient_of", "inverse": "has_excipient", "range": "Drug", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -9997,11 +9997,11 @@ "is_a": "has_part", "domain": "Drug", "slot_uri": "https://w3id.org/biolink/vocab/has_excipient", - "multivalued": true, "inherited": true, "owner": "has_excipient", "inverse": "is_excipient_of", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10032,11 +10032,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/manifestation_of", - "multivalued": true, "inherited": true, "owner": "manifestation_of", "inverse": "has_manifestation", "range": "Disease", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10046,11 +10046,11 @@ "is_a": "related_to_at_instance_level", "domain": "Disease", "slot_uri": "https://w3id.org/biolink/vocab/has_manifestation", - "multivalued": true, "inherited": true, "owner": "has_manifestation", "inverse": "manifestation_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10060,11 +10060,11 @@ "is_a": "manifestation_of", "domain": "GeneticInheritance", "slot_uri": "https://w3id.org/biolink/vocab/mode_of_inheritance_of", - "multivalued": true, "inherited": true, "owner": "mode_of_inheritance_of", "inverse": "has_mode_of_inheritance", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10085,11 +10085,11 @@ "is_a": "has_manifestation", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/has_mode_of_inheritance", - "multivalued": true, "inherited": true, "owner": "has_mode_of_inheritance", "inverse": "mode_of_inheritance_of", "range": "GeneticInheritance", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10123,11 +10123,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/produces", - "multivalued": true, "inherited": true, "owner": "produces", "inverse": "produced_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10140,11 +10140,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/produced_by", - "multivalued": true, "inherited": true, "owner": "produced_by", "inverse": "produces", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10164,11 +10164,11 @@ "is_a": "has_input", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/consumes", - "multivalued": true, "inherited": true, "owner": "consumes", "inverse": "consumed_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10178,11 +10178,11 @@ "is_a": "is_input_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/consumed_by", - "multivalued": true, "inherited": true, "owner": "consumed_by", "inverse": "consumes", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10219,11 +10219,11 @@ "is_a": "related_to_at_instance_level", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/temporally_related_to", - "multivalued": true, "inherited": true, "owner": "temporally_related_to", "symmetric": true, "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10263,11 +10263,11 @@ "is_a": "temporally_related_to", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/precedes", - "multivalued": true, "inherited": true, "owner": "precedes", "inverse": "preceded_by", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10293,11 +10293,11 @@ "is_a": "temporally_related_to", "domain": "Occurrent", "slot_uri": "https://w3id.org/biolink/vocab/preceded_by", - "multivalued": true, "inherited": true, "owner": "preceded_by", "inverse": "precedes", "range": "Occurrent", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10319,11 +10319,11 @@ "is_a": "has_part", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_variant_part", - "multivalued": true, "inherited": true, "owner": "has_variant_part", "inverse": "variant_part_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10333,11 +10333,11 @@ "is_a": "part_of", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/variant_part_of", - "multivalued": true, "inherited": true, "owner": "variant_part_of", "inverse": "has_variant_part", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10357,11 +10357,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/related_condition", - "multivalued": true, "inherited": true, "owner": "related_condition", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10387,11 +10387,11 @@ "is_a": "related_to_at_instance_level", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_sequence_variant_of", - "multivalued": true, "inherited": true, "owner": "is_sequence_variant_of", "inverse": "has_sequence_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10402,11 +10402,11 @@ "is_a": "related_to_at_instance_level", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_sequence_variant", - "multivalued": true, "inherited": true, "owner": "has_sequence_variant", "inverse": "is_sequence_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10427,11 +10427,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_missense_variant_of", - "multivalued": true, "inherited": true, "owner": "is_missense_variant_of", "inverse": "has_missense_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10442,11 +10442,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_missense_variant", - "multivalued": true, "inherited": true, "owner": "has_missense_variant", "inverse": "is_missense_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10467,11 +10467,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_synonymous_variant_of", - "multivalued": true, "inherited": true, "owner": "is_synonymous_variant_of", "inverse": "has_synonymous_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10485,11 +10485,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_synonymous_variant", - "multivalued": true, "inherited": true, "owner": "has_synonymous_variant", "inverse": "is_synonymous_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10510,11 +10510,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_nonsense_variant_of", - "multivalued": true, "inherited": true, "owner": "is_nonsense_variant_of", "inverse": "has_nonsense_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10525,11 +10525,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_nonsense_variant", - "multivalued": true, "inherited": true, "owner": "has_nonsense_variant", "inverse": "is_nonsense_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10555,11 +10555,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_frameshift_variant_of", - "multivalued": true, "inherited": true, "owner": "is_frameshift_variant_of", "inverse": "has_frameshift_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10575,11 +10575,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_frameshift_variant", - "multivalued": true, "inherited": true, "owner": "has_frameshift_variant", "inverse": "is_frameshift_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10600,11 +10600,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_splice_site_variant_of", - "multivalued": true, "inherited": true, "owner": "is_splice_site_variant_of", "inverse": "has_splice_site_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10619,11 +10619,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_splice_site_variant", - "multivalued": true, "inherited": true, "owner": "has_splice_site_variant", "inverse": "is_splice_site_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10641,11 +10641,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_nearby_variant_of", - "multivalued": true, "inherited": true, "owner": "is_nearby_variant_of", "inverse": "has_nearby_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10663,11 +10663,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_nearby_variant", - "multivalued": true, "inherited": true, "owner": "has_nearby_variant", "inverse": "is_nearby_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10685,11 +10685,11 @@ "is_a": "is_sequence_variant_of", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/is_non_coding_variant_of", - "multivalued": true, "inherited": true, "owner": "is_non_coding_variant_of", "inverse": "has_non_coding_variant", "range": "GenomicEntity", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10700,11 +10700,11 @@ "is_a": "has_sequence_variant", "domain": "GenomicEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_non_coding_variant", - "multivalued": true, "inherited": true, "owner": "has_non_coding_variant", "inverse": "is_non_coding_variant_of", "range": "SequenceVariant", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10726,11 +10726,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/disease_has_basis_in", - "multivalued": true, "inherited": true, "owner": "disease_has_basis_in", "inverse": "occurs_in_disease", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10740,11 +10740,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/occurs_in_disease", - "multivalued": true, "inherited": true, "owner": "occurs_in_disease", "inverse": "disease_has_basis_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10765,11 +10765,11 @@ "is_a": "affects", "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/has_adverse_event", - "multivalued": true, "inherited": true, "owner": "has_adverse_event", "inverse": "adverse_event_of", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10779,11 +10779,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/adverse_event_of", - "multivalued": true, "inherited": true, "owner": "adverse_event_of", "inverse": "has_adverse_event", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10811,11 +10811,11 @@ "is_a": "affects", "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/has_side_effect", - "multivalued": true, "inherited": true, "owner": "has_side_effect", "inverse": "is_side_effect_of", "range": "DiseaseOrPhenotypicFeature", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10825,11 +10825,11 @@ "is_a": "affected_by", "domain": "DiseaseOrPhenotypicFeature", "slot_uri": "https://w3id.org/biolink/vocab/is_side_effect_of", - "multivalued": true, "inherited": true, "owner": "is_side_effect_of", "inverse": "has_side_effect", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10859,11 +10859,11 @@ "is_a": "related_to_at_instance_level", "domain": "ChemicalOrDrugOrTreatment", "slot_uri": "https://w3id.org/biolink/vocab/contraindicated_in", - "multivalued": true, "inherited": true, "owner": "contraindicated_in", "inverse": "has_contraindication", "range": "BiologicalEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10883,11 +10883,11 @@ "is_a": "related_to_at_instance_level", "domain": "BiologicalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_contraindication", - "multivalued": true, "inherited": true, "owner": "has_contraindication", "inverse": "contraindicated_in", "range": "ChemicalOrDrugOrTreatment", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -10914,11 +10914,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_not_completed", - "multivalued": true, "inherited": true, "owner": "has_not_completed", "inverse": "not_completed_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10928,11 +10928,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/not_completed_by", - "multivalued": true, "inherited": true, "owner": "not_completed_by", "inverse": "has_not_completed", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10958,11 +10958,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_completed", - "multivalued": true, "inherited": true, "owner": "has_completed", "inverse": "completed_by", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10972,11 +10972,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/completed_by", - "multivalued": true, "inherited": true, "owner": "completed_by", "inverse": "has_completed", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -10997,11 +10997,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/in_linkage_disequilibrium_with", - "multivalued": true, "inherited": true, "owner": "in_linkage_disequilibrium_with", "symmetric": true, "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11026,11 +11026,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_increased_amount", - "multivalued": true, "inherited": true, "owner": "has_increased_amount", "inverse": "increased_amount_of", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11040,11 +11040,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/increased_amount_of", - "multivalued": true, "inherited": true, "owner": "increased_amount_of", "inverse": "has_increased_amount", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11069,11 +11069,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_decreased_amount", - "multivalued": true, "inherited": true, "owner": "has_decreased_amount", "inverse": "decreased_amount_in", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11083,11 +11083,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/decreased_amount_in", - "multivalued": true, "inherited": true, "owner": "decreased_amount_in", "inverse": "has_decreased_amount", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11116,11 +11116,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/lacks_part", - "multivalued": true, "inherited": true, "owner": "lacks_part", "inverse": "missing_from", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11130,11 +11130,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/missing_from", - "multivalued": true, "inherited": true, "owner": "missing_from", "inverse": "lacks_part", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11166,11 +11166,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/develops_from", - "multivalued": true, "inherited": true, "owner": "develops_from", "inverse": "develops_into", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11180,11 +11180,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/develops_into", - "multivalued": true, "inherited": true, "owner": "develops_into", "inverse": "develops_from", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11219,7 +11219,6 @@ "is_a": "related_to_at_instance_level", "domain": "ThingWithTaxon", "slot_uri": "https://w3id.org/biolink/vocab/in_taxon", - "multivalued": true, "inherited": true, "owner": "ThingWithTaxon", "domain_of": [ @@ -11227,6 +11226,7 @@ ], "inverse": "taxon_of", "range": "OrganismTaxon", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11264,11 +11264,11 @@ "is_a": "related_to_at_instance_level", "domain": "OrganismTaxon", "slot_uri": "https://w3id.org/biolink/vocab/taxon_of", - "multivalued": true, "inherited": true, "owner": "taxon_of", "inverse": "in_taxon", "range": "ThingWithTaxon", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -11293,11 +11293,11 @@ "is_a": "related_to_at_instance_level", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/has_molecular_consequence", - "multivalued": true, "inherited": true, "owner": "has_molecular_consequence", "inverse": "is_molecular_consequence_of", "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11307,11 +11307,11 @@ "is_a": "related_to_at_instance_level", "domain": "OntologyClass", "slot_uri": "https://w3id.org/biolink/vocab/is_molecular_consequence_of", - "multivalued": true, "inherited": true, "owner": "is_molecular_consequence_of", "inverse": "has_molecular_consequence", "range": "NamedThing", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11420,12 +11420,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11450,12 +11450,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11538,12 +11538,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_category_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11568,12 +11568,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_category_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11598,12 +11598,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_label_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11632,12 +11632,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_label_closure", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -11940,12 +11940,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/has_evidence", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "EvidenceType", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12039,12 +12039,12 @@ "is_a": "node_property", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/provided_by", - "multivalued": true, "owner": "NamedThing", "domain_of": [ "NamedThing" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12076,12 +12076,12 @@ "is_a": "knowledge_source", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/aggregator_knowledge_source", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12095,9 +12095,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_data_source", - "multivalued": true, "owner": "supporting_data_source", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12108,9 +12108,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_data_set", - "multivalued": true, "owner": "supporting_data_set", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12342,9 +12342,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_text", - "multivalued": true, "owner": "supporting_text", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12362,9 +12362,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/supporting_documents", - "multivalued": true, "owner": "supporting_documents", "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12381,9 +12381,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/subject_location_in_text", - "multivalued": true, "owner": "subject_location_in_text", "range": "integer", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12400,9 +12400,9 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/object_location_in_text", - "multivalued": true, "owner": "object_location_in_text", "range": "integer", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12592,12 +12592,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/publications", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "Publication", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12829,12 +12829,12 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/has_supporting_studies", - "multivalued": true, "owner": "Association", "domain_of": [ "Association" ], "range": "Study", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -12954,7 +12954,6 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/knowledge_level", - "ifabsent": "string(not_provided)", "owner": "Association", "domain_of": [ "Association" @@ -12992,7 +12991,6 @@ "is_a": "association_slot", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/agent_type", - "ifabsent": "string(not_provided)", "owner": "Association", "domain_of": [ "Association" @@ -13050,7 +13048,6 @@ "is_a": "category", "domain": "NamedThing", "slot_uri": "https://w3id.org/biolink/vocab/category", - "multivalued": true, "designates_type": true, "alias": "category", "owner": "NamedThing", @@ -13062,6 +13059,7 @@ "usage_slot_name": "category", "range": "uriorcurie", "required": true, + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13242,7 +13240,6 @@ ], "domain": "Publication", "slot_uri": "http://purl.org/dc/terms/type", - "multivalued": true, "alias": "publication type", "owner": "Publication", "domain_of": [ @@ -13252,6 +13249,7 @@ "usage_slot_name": "publication type", "range": "string", "required": true, + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13265,7 +13263,6 @@ "is_a": "pages", "domain": "Publication", "slot_uri": "https://w3id.org/biolink/vocab/pages", - "multivalued": true, "alias": "pages", "owner": "Publication", "domain_of": [ @@ -13274,6 +13271,7 @@ "is_usage_slot": true, "usage_slot_name": "pages", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13319,7 +13317,6 @@ "is_a": "type", "domain": "Book", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "multivalued": true, "alias": "type", "owner": "Book", "domain_of": [ @@ -13328,6 +13325,7 @@ "is_usage_slot": true, "usage_slot_name": "type", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13400,7 +13398,6 @@ "is_a": "type", "domain": "Serial", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "multivalued": true, "alias": "type", "owner": "Serial", "domain_of": [ @@ -13409,6 +13406,7 @@ "is_usage_slot": true, "usage_slot_name": "type", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13565,7 +13563,6 @@ "is_a": "has_input", "domain": "MolecularActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_input", - "multivalued": true, "inherited": true, "alias": "has input", "owner": "MolecularActivity", @@ -13575,6 +13572,7 @@ "is_usage_slot": true, "usage_slot_name": "has input", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13616,7 +13614,6 @@ "is_a": "has_output", "domain": "MolecularActivity", "slot_uri": "https://w3id.org/biolink/vocab/has_output", - "multivalued": true, "inherited": true, "alias": "has output", "owner": "MolecularActivity", @@ -13626,6 +13623,7 @@ "is_usage_slot": true, "usage_slot_name": "has output", "range": "MolecularEntity", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13650,7 +13648,6 @@ "is_a": "enabled_by", "domain": "MolecularActivity", "slot_uri": "https://w3id.org/biolink/vocab/enabled_by", - "multivalued": true, "inherited": true, "alias": "enabled by", "owner": "MolecularActivity", @@ -13660,6 +13657,7 @@ "is_usage_slot": true, "usage_slot_name": "enabled by", "range": "MacromolecularMachineMixin", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -13756,7 +13754,6 @@ "is_a": "has_attribute", "domain": "OrganismalEntity", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", - "multivalued": true, "alias": "has attribute", "owner": "OrganismalEntity", "domain_of": [ @@ -13765,6 +13762,7 @@ "is_usage_slot": true, "usage_slot_name": "has attribute", "range": "Attribute", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -13813,7 +13811,6 @@ "is_a": "has_gene", "domain": "SequenceVariant", "slot_uri": "https://w3id.org/biolink/vocab/has_gene", - "multivalued": true, "alias": "has gene", "owner": "SequenceVariant", "domain_of": [ @@ -13822,6 +13819,7 @@ "is_usage_slot": true, "usage_slot_name": "has gene", "range": "Gene", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14005,7 +14003,6 @@ "is_a": "has_attribute", "domain": "ClinicalFinding", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", - "multivalued": true, "alias": "has attribute", "owner": "ClinicalFinding", "domain_of": [ @@ -14014,6 +14011,7 @@ "is_usage_slot": true, "usage_slot_name": "has attribute", "range": "ClinicalAttribute", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14109,7 +14107,6 @@ "is_a": "has_attribute", "domain": "SocioeconomicExposure", "slot_uri": "https://w3id.org/biolink/vocab/has_attribute", - "multivalued": true, "alias": "has attribute", "owner": "SocioeconomicExposure", "domain_of": [ @@ -14119,6 +14116,7 @@ "usage_slot_name": "has attribute", "range": "SocioeconomicAttribute", "required": true, + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14136,7 +14134,6 @@ "is_a": "type", "domain": "Association", "slot_uri": "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", - "multivalued": true, "alias": "type", "owner": "Association", "domain_of": [ @@ -14145,6 +14142,7 @@ "is_usage_slot": true, "usage_slot_name": "type", "range": "string", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14158,7 +14156,6 @@ "is_a": "category", "domain": "Association", "slot_uri": "https://w3id.org/biolink/vocab/category", - "multivalued": true, "designates_type": true, "alias": "category", "owner": "Association", @@ -14169,6 +14166,7 @@ "is_usage_slot": true, "usage_slot_name": "category", "range": "uriorcurie", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -14410,7 +14408,6 @@ "is_a": "qualifiers", "domain": "ContributorAssociation", "slot_uri": "https://w3id.org/biolink/vocab/qualifiers", - "multivalued": true, "alias": "qualifiers", "owner": "ContributorAssociation", "domain_of": [ @@ -14419,6 +14416,7 @@ "is_usage_slot": true, "usage_slot_name": "qualifiers", "range": "OntologyClass", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -15767,7 +15765,6 @@ "is_a": "catalyst_qualifier", "domain": "ChemicalToChemicalDerivationAssociation", "slot_uri": "https://w3id.org/biolink/vocab/catalyst_qualifier", - "multivalued": true, "alias": "catalyst qualifier", "owner": "ChemicalToChemicalDerivationAssociation", "domain_of": [ @@ -15776,6 +15773,7 @@ "is_usage_slot": true, "usage_slot_name": "catalyst qualifier", "range": "MacromolecularMachineMixin", + "multivalued": true, "inlined": true, "@type": "SlotDefinition" }, @@ -19790,7 +19788,6 @@ "is_a": "has_evidence", "domain": "DruggableGeneToDiseaseAssociation", "slot_uri": "https://w3id.org/biolink/vocab/has_evidence", - "multivalued": true, "alias": "has evidence", "owner": "DruggableGeneToDiseaseAssociation", "domain_of": [ @@ -19799,6 +19796,7 @@ "is_usage_slot": true, "usage_slot_name": "has evidence", "range": "DruggableGeneCategoryEnum", + "multivalued": true, "@type": "SlotDefinition" }, { @@ -35719,9 +35717,9 @@ ], "metamodel_version": "1.7.0", "source_file": "biolink_model.yaml", - "source_file_date": "2024-10-10T17:38:41", - "source_file_size": 401126, - "generation_date": "2024-10-10T17:38:46", + "source_file_date": "2024-10-10T16:29:50", + "source_file_size": 401056, + "generation_date": "2024-10-10T16:29:57", "@type": "SchemaDefinition", "@context": [ "project/jsonld/biolink_model.context.jsonld", diff --git a/project/jsonschema/biolink_model.schema.json b/project/jsonschema/biolink_model.schema.json index a2f4ad87e..1306a9e67 100644 --- a/project/jsonschema/biolink_model.schema.json +++ b/project/jsonschema/biolink_model.schema.json @@ -16,26 +16,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -46,46 +61,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -111,22 +150,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -134,38 +185,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -181,14 +250,20 @@ "properties": { "address": { "description": "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).", - "type": "string" + "type": [ + "string", + "null" + ] }, "affiliation": { "description": "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -202,22 +277,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.", @@ -225,38 +312,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -297,22 +402,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -323,46 +440,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -378,7 +519,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -389,7 +533,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -399,36 +546,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -436,7 +601,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -444,15 +612,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the structure at an earlier time", @@ -460,48 +637,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -509,32 +713,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the structure at a later time", @@ -542,44 +761,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -599,7 +839,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -610,7 +853,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -620,36 +866,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -657,7 +921,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -665,15 +932,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the whole", @@ -681,48 +957,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -730,32 +1033,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the part", @@ -763,44 +1081,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -845,7 +1184,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -860,29 +1202,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -890,50 +1250,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iso_abbreviation": { "description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", - "type": "string" + "type": [ + "string", + "null" + ] }, "issue": { "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -947,35 +1334,53 @@ "type": "string" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -993,7 +1398,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -1004,7 +1412,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -1014,36 +1425,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1051,7 +1480,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -1059,15 +1491,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -1075,48 +1516,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -1124,32 +1592,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -1157,44 +1640,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1224,22 +1728,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -1247,14 +1763,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1262,38 +1784,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1320,22 +1860,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1346,46 +1898,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1411,43 +1987,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1458,46 +2055,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1513,7 +2134,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -1524,7 +2148,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -1534,55 +2161,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1590,7 +2250,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -1598,15 +2261,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "behavioral feature that is the object of the association", @@ -1614,25 +2286,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -1643,27 +2327,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -1671,40 +2373,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "behavior that is the subject of the association", @@ -1712,25 +2435,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -1741,23 +2476,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1787,22 +2534,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -1810,14 +2569,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1825,43 +2590,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1888,22 +2674,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -1914,46 +2712,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -1985,43 +2807,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2032,46 +2875,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2097,43 +2964,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2144,46 +3032,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2209,22 +3121,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -2232,14 +3156,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2247,38 +3177,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2305,22 +3253,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -2328,14 +3288,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2343,43 +3309,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2399,7 +3386,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -2414,29 +3404,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Books should have industry-standard identifier such as from ISBN.", @@ -2444,42 +3452,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -2489,32 +3518,47 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "description": "Should generally be set to an ontology class defined term for 'book'.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2534,7 +3578,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -2548,34 +3595,55 @@ }, "chapter": { "description": "chapter of a book", - "type": "string" + "type": [ + "string", + "null" + ] }, "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -2583,42 +3651,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -2632,35 +3721,53 @@ "type": "string" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2688,22 +3795,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2714,46 +3833,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -2769,7 +3912,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -2780,7 +3926,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -2790,55 +3939,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -2846,7 +4028,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -2854,15 +4039,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -2870,25 +4064,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -2899,27 +4105,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -2927,40 +4151,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "the case (e.g. patient) that has the property", @@ -2968,25 +4213,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -2997,23 +4254,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3033,7 +4302,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -3044,7 +4316,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3054,55 +4329,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3110,7 +4418,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -3118,15 +4429,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -3134,25 +4454,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -3163,27 +4495,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -3191,40 +4541,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -3236,21 +4607,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -3261,23 +4641,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3332,22 +4724,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3358,46 +4762,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3423,22 +4851,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3449,46 +4889,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3504,7 +4968,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -3515,7 +4982,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3525,40 +4995,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3566,7 +5057,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -3574,15 +5068,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -3590,25 +5093,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -3619,27 +5134,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -3647,36 +5180,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "A cell line derived from an organismal entity with a disease state that is used as a model of that disease.", @@ -3684,25 +5235,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -3713,23 +5276,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3749,7 +5324,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -3760,7 +5338,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -3770,36 +5351,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -3807,7 +5406,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -3815,15 +5417,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease or phenotype", @@ -3831,48 +5442,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -3880,32 +5518,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -3913,44 +5566,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -3980,22 +5654,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4006,46 +5692,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4071,22 +5781,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4097,46 +5819,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4152,7 +5898,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -4163,11 +5912,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "anatomical_context_qualifier": { "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", - "type": "string" + "type": [ + "string", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4177,7 +5932,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", @@ -4185,32 +5943,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4218,7 +5991,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -4226,15 +6002,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -4246,24 +6031,36 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -4278,11 +6075,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -4290,19 +6093,31 @@ }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -4310,40 +6125,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -4355,24 +6191,36 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum", @@ -4391,11 +6239,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -4404,14 +6258,20 @@ "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4434,7 +6294,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4448,29 +6311,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4478,50 +6356,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4537,7 +6442,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -4548,7 +6456,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4558,36 +6469,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4595,7 +6524,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -4603,15 +6535,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -4619,48 +6560,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -4668,32 +6636,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -4701,44 +6684,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -4766,7 +6770,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -4777,7 +6784,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -4787,36 +6797,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -4824,7 +6852,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -4832,15 +6863,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -4848,21 +6888,30 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -4873,27 +6922,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "the direction is always from regulator to regulated", @@ -4901,32 +6968,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -4934,44 +7016,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5001,22 +7104,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -5024,14 +7139,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5039,43 +7160,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5092,7 +7234,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -5103,11 +7248,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "anatomical_context_qualifier": { "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", - "type": "string" + "type": [ + "string", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5117,36 +7268,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5154,7 +7323,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -5162,15 +7334,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -5178,24 +7359,36 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_form_or_variant_qualifier": { "$ref": "#/$defs/ChemicalOrGeneOrGeneProductFormOrVariantEnum", @@ -5206,11 +7399,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -5218,19 +7417,31 @@ }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -5238,32 +7449,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the chemical entity or entity that is an interactor", @@ -5271,24 +7497,36 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum", @@ -5303,11 +7541,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -5316,14 +7560,20 @@ "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5346,7 +7596,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5360,11 +7613,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -5372,21 +7631,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -5398,61 +7666,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5472,7 +7773,10 @@ }, "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -5483,7 +7787,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5493,36 +7800,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5530,7 +7855,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -5538,15 +7866,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease or phenotype", @@ -5554,48 +7891,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -5603,32 +7967,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -5636,44 +8015,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5697,7 +8097,10 @@ }, "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -5708,7 +8111,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -5718,36 +8124,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5755,7 +8179,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -5763,15 +8190,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease or phenotype", @@ -5779,48 +8215,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -5828,32 +8291,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -5861,44 +8339,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -5942,22 +8441,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -5965,14 +8476,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -5980,38 +8497,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6028,7 +8563,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6039,7 +8577,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6049,36 +8590,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6086,7 +8645,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6094,15 +8656,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the chemical element that is the target of the statement", @@ -6110,48 +8681,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6159,32 +8757,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -6192,44 +8805,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6249,7 +8883,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6260,14 +8897,20 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "catalyst_qualifier": { "description": "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical.", "items": { "$ref": "#/$defs/MacromolecularMachineMixin" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6277,36 +8920,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6314,7 +8975,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6322,15 +8986,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the downstream chemical entity", @@ -6338,48 +9011,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6387,32 +9087,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the upstream chemical entity", @@ -6420,44 +9135,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6477,7 +9213,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6488,7 +9227,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6498,36 +9240,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6535,7 +9295,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6543,15 +9306,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the disease or phenotype that is affected by the chemical", @@ -6559,48 +9331,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6608,32 +9407,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/ChemicalEntityOrGeneOrGeneProduct", @@ -6641,44 +9455,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6698,7 +9533,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -6709,7 +9547,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -6719,36 +9560,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6756,7 +9615,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -6764,15 +9626,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the pathway that is affected by the chemical", @@ -6780,48 +9651,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -6829,32 +9727,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the chemical entity that is affecting the pathway", @@ -6862,44 +9775,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -6930,29 +9864,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -6960,44 +9912,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7036,22 +10012,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -7059,14 +10047,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7074,38 +10068,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7132,22 +10144,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -7155,14 +10179,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7170,38 +10200,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7228,22 +10276,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7251,38 +10311,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7308,22 +10386,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7334,46 +10424,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7399,22 +10513,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7422,38 +10548,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7479,22 +10623,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -7502,14 +10658,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7517,38 +10679,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7575,22 +10755,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -7598,14 +10790,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7613,38 +10811,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7671,22 +10887,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7694,38 +10922,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7751,26 +10997,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7781,46 +11042,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7846,22 +11131,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7872,46 +11169,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -7938,29 +11259,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -7968,44 +11307,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8031,22 +11394,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -8054,14 +11429,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8069,38 +11450,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8120,7 +11519,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8134,11 +11536,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -8146,21 +11554,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -8172,61 +11589,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8253,29 +11703,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8283,44 +11751,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8347,29 +11839,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8377,44 +11887,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8430,7 +11964,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -8441,7 +11978,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8451,36 +11991,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8488,7 +12046,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -8496,15 +12057,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "agent helping to realise the given entity (e.g. such as a publication)", @@ -8512,48 +12082,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'", @@ -8561,32 +12158,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "information content entity which an agent has helped realise", @@ -8594,44 +12206,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8651,7 +12284,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -8662,7 +12298,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -8672,55 +12311,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8728,7 +12400,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -8736,15 +12411,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -8752,25 +12436,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -8781,27 +12477,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -8809,40 +12523,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -8854,21 +12589,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -8879,23 +12623,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -8926,29 +12682,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -8956,44 +12730,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9020,32 +12818,53 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "distribution_download_url": { - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9053,44 +12872,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9117,29 +12960,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9147,50 +13008,80 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "source_logo": { - "type": "string" + "type": [ + "string", + "null" + ] }, "source_web_page": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9217,83 +13108,134 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_dataset": { - "type": "string" + "type": [ + "string", + "null" + ] }, "has_distribution": { - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", "type": "string" }, "ingest_date": { - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9319,22 +13261,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9342,38 +13296,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9399,22 +13371,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9422,38 +13406,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9490,22 +13492,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9516,46 +13530,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9581,22 +13619,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9607,46 +13657,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9672,22 +13746,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -9695,14 +13781,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9710,43 +13802,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9769,7 +13882,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -9780,7 +13896,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -9790,36 +13909,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -9827,7 +13964,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -9835,15 +13975,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "genetic inheritance associated with the specified disease or phenotypic feature.", @@ -9851,48 +14000,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -9900,32 +14076,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "disease or phenotype", @@ -9933,44 +14124,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -9990,7 +14202,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -10001,7 +14216,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10011,36 +14229,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10048,7 +14284,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -10056,15 +14295,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "anatomical entity in which the disease or feature is found.", @@ -10072,48 +14320,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -10121,32 +14396,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "disease or phenotype", @@ -10154,44 +14444,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10211,7 +14522,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -10222,7 +14536,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10232,36 +14549,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10269,7 +14604,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -10277,15 +14615,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -10293,48 +14640,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -10342,32 +14716,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "disease class", @@ -10375,44 +14764,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10432,7 +14842,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -10443,7 +14856,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10453,55 +14869,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10509,7 +14958,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -10517,15 +14969,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -10533,25 +14994,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -10562,31 +15035,52 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "onset_qualifier": { "description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -10594,40 +15088,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "disease class", @@ -10635,25 +15150,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -10664,23 +15191,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10703,7 +15242,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10717,11 +15259,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -10729,21 +15277,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -10755,61 +15312,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10855,22 +15445,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -10878,14 +15480,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -10893,43 +15501,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -10949,7 +15578,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -10964,29 +15596,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -10994,42 +15644,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -11039,31 +15710,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11080,7 +15766,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -11091,7 +15780,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11101,36 +15793,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11138,7 +15848,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -11146,15 +15859,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -11162,48 +15884,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -11211,32 +15960,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the drug that is an interactor", @@ -11244,44 +16008,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11311,22 +16096,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -11337,18 +16134,27 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11356,43 +16162,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11420,7 +16247,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -11431,7 +16261,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11441,55 +16274,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "$ref": "#/$defs/DruggableGeneCategoryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11497,7 +16363,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -11505,15 +16374,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -11521,25 +16399,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -11550,27 +16440,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -11578,40 +16486,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -11623,21 +16552,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -11648,23 +16586,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11684,7 +16634,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -11695,7 +16648,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11705,7 +16661,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "clinical_approval_status": { "$ref": "#/$defs/ClinicalApprovalStatusEnum", @@ -11713,32 +16672,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11746,7 +16720,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -11754,18 +16731,27 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "max_research_phase": { "$ref": "#/$defs/ResearchPhaseEnum" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -11773,48 +16759,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -11822,32 +16835,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -11855,44 +16883,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -11912,7 +16961,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -11923,7 +16975,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -11933,7 +16988,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "clinical_approval_status": { "$ref": "#/$defs/ClinicalApprovalStatusEnum", @@ -11941,32 +16999,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -11974,7 +17047,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -11982,18 +17058,27 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "max_research_phase": { "$ref": "#/$defs/ResearchPhaseEnum" }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -12001,48 +17086,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -12050,32 +17162,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -12083,44 +17210,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12150,22 +17298,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -12173,14 +17333,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12188,43 +17354,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12251,22 +17438,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12274,38 +17473,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12324,7 +17541,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -12338,29 +17558,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12368,50 +17603,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12437,22 +17699,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12460,38 +17734,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12523,22 +17815,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12546,38 +17850,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12604,29 +17926,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12634,44 +17974,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12697,22 +18061,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12723,46 +18099,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12778,7 +18178,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -12789,7 +18192,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -12799,36 +18205,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -12836,7 +18260,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -12844,15 +18271,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -12860,48 +18296,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -12909,32 +18372,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -12942,44 +18420,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -12999,7 +18498,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -13010,7 +18512,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13020,36 +18525,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13057,7 +18580,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -13065,15 +18591,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/Outcome", @@ -13081,52 +18616,82 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "population_context_qualifier": { "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -13134,32 +18699,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -13167,49 +18747,73 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "temporal_context_qualifier": { "description": "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier.", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13229,7 +18833,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -13240,7 +18847,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13250,55 +18860,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13306,7 +18949,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -13314,15 +18960,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -13330,25 +18985,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -13359,27 +19026,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -13387,40 +19072,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -13428,25 +19134,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -13457,23 +19175,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13507,7 +19237,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13521,11 +19254,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -13533,21 +19272,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -13559,61 +19307,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13632,7 +19413,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13646,29 +19430,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13676,50 +19475,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13735,7 +19561,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -13746,7 +19575,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -13756,36 +19588,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13793,7 +19643,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -13801,15 +19654,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -13817,48 +19679,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -13866,32 +19755,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -13899,44 +19803,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -13966,22 +19891,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -13992,46 +19929,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14057,26 +20018,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14087,50 +20063,77 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "symbol": { "description": "Symbol for a particular thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14146,7 +20149,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -14157,11 +20163,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "anatomical_context_qualifier": { "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", - "type": "string" + "type": [ + "string", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14171,7 +20183,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", @@ -14179,32 +20194,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14212,7 +20242,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -14220,15 +20253,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -14240,24 +20282,36 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_derivative_qualifier": { "$ref": "#/$defs/ChemicalEntityDerivativeEnum", @@ -14276,11 +20330,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -14288,19 +20348,31 @@ }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -14308,40 +20380,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -14353,28 +20446,43 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_derivative_qualifier": { "description": "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier \u2018metabolite\u2019 combines with a \u2018Chemical X\u2019 core concept to express the composed concept \u2018a metabolite of Chemical X\u2019. This qualifier is for the subject of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14389,11 +20497,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_part_qualifier": { "$ref": "#/$defs/GeneOrGeneProductOrChemicalPartQualifierEnum", @@ -14402,14 +20516,20 @@ "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14429,7 +20549,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -14440,7 +20563,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14450,55 +20576,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14506,7 +20665,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -14514,15 +20676,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -14530,25 +20701,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14559,27 +20742,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -14587,40 +20788,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -14632,21 +20854,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14657,23 +20888,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14703,29 +20946,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14736,46 +20994,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -14791,7 +21073,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -14802,7 +21087,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -14812,55 +21100,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -14868,7 +21189,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -14876,15 +21200,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -14892,25 +21225,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -14921,27 +21266,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -14949,40 +21312,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -14994,21 +21378,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15016,30 +21409,45 @@ }, "subject_form_or_variant_qualifier": { "description": "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier \u2018mutation\u2019 combines with the core concept \u2018Gene X\u2019 to express the compose concept \u2018a mutation of Gene X\u2019. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -15134,7 +21542,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -15145,7 +21556,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15155,36 +21569,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15192,7 +21624,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -15200,15 +21635,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -15220,21 +21664,30 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15245,27 +21698,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -15273,14 +21744,20 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", @@ -15288,25 +21765,37 @@ }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -15314,44 +21803,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -15374,7 +21884,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -15385,7 +21898,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15395,55 +21911,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15451,7 +22000,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -15459,15 +22011,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -15475,25 +22036,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15504,27 +22077,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -15532,40 +22123,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -15577,21 +22189,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15602,23 +22223,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -15638,7 +22271,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -15649,7 +22285,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15659,55 +22298,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15715,7 +22387,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -15723,15 +22398,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -15739,25 +22423,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15768,27 +22464,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -15796,40 +22510,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -15841,21 +22576,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -15866,23 +22610,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -15902,7 +22658,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -15913,7 +22672,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -15923,36 +22685,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -15960,7 +22740,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -15968,15 +22751,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "location in which the gene is expressed", @@ -15984,48 +22776,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "expression relationship", @@ -16033,40 +22852,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "quantifier_qualifier": { "description": "can be used to indicate magnitude, or also ranking", - "type": "string" + "type": [ + "string", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stage_qualifier": { "description": "stage at which the gene is expressed in the site", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16074,44 +22914,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -16131,7 +22992,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16142,7 +23006,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16152,40 +23019,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "expression_site": { "description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16193,7 +23081,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16201,15 +23092,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16217,52 +23117,82 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "phenotypic_state": { "description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -16270,40 +23200,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "quantifier_qualifier": { "description": "Optional quantitative value indicating degree of expression.", - "type": "string" + "type": [ + "string", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stage_qualifier": { "description": "stage during which gene or protein expression of takes place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16311,44 +23262,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -16368,7 +23340,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16379,7 +23354,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16389,36 +23367,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16426,7 +23422,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16434,15 +23433,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -16450,48 +23458,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "membership of the gene in the given gene family.", @@ -16499,32 +23534,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -16532,44 +23582,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -16589,7 +23660,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16600,7 +23674,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16610,36 +23687,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16647,7 +23742,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16655,15 +23753,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16671,48 +23778,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "homology relationship type", @@ -16720,32 +23854,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -16753,44 +23902,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -16810,7 +23980,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -16821,7 +23994,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -16831,36 +24007,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -16868,7 +24062,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -16876,15 +24073,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneProductMixin", @@ -16892,48 +24098,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -16941,32 +24174,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -16974,44 +24222,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17031,7 +24300,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -17042,7 +24314,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17052,36 +24327,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17089,7 +24382,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -17097,15 +24393,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -17113,48 +24418,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -17162,32 +24494,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "gene, product or macromolecular complex that has the function associated with the GO term", @@ -17195,44 +24542,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17252,7 +24620,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -17263,7 +24634,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17273,36 +24647,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17310,7 +24702,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -17318,15 +24713,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the pathway that includes or is affected by the gene or gene product", @@ -17334,48 +24738,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -17383,32 +24814,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -17416,44 +24862,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17473,7 +24940,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -17484,7 +24954,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -17494,55 +24967,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17550,7 +25056,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -17558,15 +25067,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -17574,25 +25092,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -17603,27 +25133,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -17631,40 +25179,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -17676,21 +25245,30 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -17701,23 +25279,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17747,22 +25337,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17773,46 +25375,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17838,26 +25464,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17868,46 +25509,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -17933,22 +25598,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -17956,25 +25633,37 @@ }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -17985,51 +25674,78 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18046,7 +25762,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18057,7 +25776,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18067,19 +25789,31 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "end_interbase_coordinate": { "description": "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on.", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "genome_build": { "$ref": "#/$defs/StrandEnum", @@ -18090,21 +25824,30 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18112,7 +25855,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18120,15 +25866,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -18136,48 +25891,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "phase": { "$ref": "#/$defs/PhaseEnum", @@ -18189,36 +25971,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "start_interbase_coordinate": { "description": "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0).", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "strand": { "$ref": "#/$defs/StrandEnum", @@ -18230,44 +26030,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18297,29 +26118,47 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_zygosity": { - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18330,46 +26169,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18385,7 +26248,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18396,7 +26262,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18406,40 +26275,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18447,7 +26337,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18455,15 +26348,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -18471,25 +26373,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18500,27 +26414,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -18528,36 +26460,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "A genotype that has a role in modeling the disease.", @@ -18565,25 +26515,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18594,23 +26556,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18630,7 +26604,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18641,7 +26618,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18651,40 +26631,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18692,7 +26693,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18700,15 +26704,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "a disease that is associated with that genotype", @@ -18716,25 +26729,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18745,27 +26770,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "E.g. is pathogenic for", @@ -18773,36 +26816,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "a genotype that is associated in some way with a disease state", @@ -18810,25 +26871,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -18839,23 +26912,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -18875,7 +26960,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -18886,7 +26974,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -18896,36 +26987,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -18933,7 +27042,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -18941,15 +27053,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "gene implicated in genotype", @@ -18957,48 +27078,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "the relationship type used to connect genotype to gene", @@ -19006,32 +27154,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "parent genotype", @@ -19039,44 +27202,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19096,7 +27280,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -19107,7 +27294,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19117,36 +27307,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19154,7 +27362,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -19162,15 +27373,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "child genotype", @@ -19178,48 +27398,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -19227,32 +27474,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "parent genotype", @@ -19260,44 +27522,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19317,7 +27600,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -19328,7 +27614,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19338,55 +27627,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19394,7 +27716,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -19402,15 +27727,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -19418,25 +27752,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -19447,27 +27793,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -19475,40 +27839,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "genotype that is associated with the phenotypic feature", @@ -19516,25 +27901,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -19545,23 +27942,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19581,7 +27990,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -19592,7 +28004,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -19602,36 +28017,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19639,7 +28072,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -19647,15 +28083,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "gene implicated in genotype", @@ -19663,48 +28108,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "the relationship type used to connect genotype to gene", @@ -19712,32 +28184,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "parent genotype", @@ -19745,44 +28232,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19812,22 +28320,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -19835,14 +28355,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19850,38 +28376,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -19908,22 +28452,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -19931,14 +28487,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -19946,43 +28508,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20009,22 +28592,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20032,46 +28627,70 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "latitude": { "description": "latitude", - "type": "number" + "type": [ + "number", + "null" + ] }, "longitude": { "description": "longitude", - "type": "number" + "type": [ + "number", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20097,22 +28716,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20120,51 +28751,78 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "latitude": { "description": "latitude", - "type": "number" + "type": [ + "number", + "null" + ] }, "longitude": { "description": "longitude", - "type": "number" + "type": [ + "number", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20190,22 +28848,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20216,46 +28886,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20281,26 +28975,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20311,46 +29020,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20376,22 +29109,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20399,38 +29144,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20462,22 +29225,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20488,46 +29263,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20553,22 +29352,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20579,46 +29390,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20634,7 +29469,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -20645,7 +29483,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -20655,36 +29496,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20692,7 +29551,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -20700,15 +29562,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -20716,48 +29587,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -20765,32 +29663,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -20798,44 +29711,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20865,22 +29799,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -20891,46 +29837,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -20949,7 +29919,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -20964,29 +29937,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -20994,50 +29985,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iso_abbreviation": { "description": "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.", - "type": "string" + "type": [ + "string", + "null" + ] }, "issue": { "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -21051,35 +30069,53 @@ "type": "string" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21120,22 +30156,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21146,46 +30194,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21212,29 +30284,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21242,44 +30332,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21315,22 +30429,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21341,46 +30467,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21396,7 +30546,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -21407,7 +30560,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -21417,36 +30573,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21454,7 +30628,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -21462,15 +30639,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -21478,48 +30664,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -21527,32 +30740,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -21560,44 +30788,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21617,7 +30866,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -21628,7 +30880,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -21638,36 +30893,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21675,7 +30948,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -21683,15 +30959,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -21699,48 +30984,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -21748,32 +31060,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -21781,44 +31108,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -21838,7 +31186,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -21849,7 +31200,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -21859,36 +31213,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -21896,7 +31268,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -21904,15 +31279,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "class describing the activity, process or localization of the gene product", @@ -21920,48 +31304,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -21969,32 +31380,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/MacromolecularMachineMixin", @@ -22002,44 +31428,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22069,22 +31516,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22095,46 +31554,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22160,22 +31643,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22183,38 +31678,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22230,7 +31743,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -22241,7 +31757,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22251,36 +31770,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22288,7 +31825,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -22296,15 +31836,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.", @@ -22312,48 +31861,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "derivation relationship", @@ -22361,32 +31937,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the material sample being described", @@ -22394,44 +31985,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22451,7 +32063,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -22462,7 +32077,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22472,36 +32090,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22509,7 +32145,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -22517,15 +32156,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease or phenotype", @@ -22533,48 +32181,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -22582,32 +32257,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the material sample being described", @@ -22615,44 +32305,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22682,22 +32393,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22708,46 +32431,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22773,43 +32520,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "The gene product, gene, or complex that catalyzes the reaction", "items": { "$ref": "#/$defs/MacromolecularMachineMixin" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "A chemical entity that is the input for the reaction", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "A chemical entity that is the output for the reaction", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22820,46 +32588,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -22875,7 +32667,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -22886,7 +32681,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -22896,36 +32694,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -22933,7 +32749,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -22941,15 +32760,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -22957,48 +32785,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -23006,32 +32861,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23039,44 +32909,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23096,7 +32987,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -23107,7 +33001,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23117,36 +33014,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23154,7 +33069,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23162,15 +33080,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23178,48 +33105,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -23227,32 +33181,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23260,44 +33229,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23317,7 +33307,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -23328,7 +33321,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23338,36 +33334,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23375,7 +33389,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23383,15 +33400,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23399,48 +33425,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -23448,32 +33501,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23481,44 +33549,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23541,7 +33630,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23555,29 +33647,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23585,54 +33692,84 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_metabolite": { "description": "indicates whether a molecular entity is a metabolite", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23651,7 +33788,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23665,11 +33805,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -23677,21 +33823,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -23703,61 +33858,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23789,22 +33977,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23812,38 +34012,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -23859,7 +34077,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -23870,7 +34091,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -23880,36 +34104,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -23917,7 +34159,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -23925,15 +34170,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -23941,59 +34195,95 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "population_context_qualifier": { "description": "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -24001,32 +34291,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -24034,51 +34339,78 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24108,22 +34440,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24134,46 +34478,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24192,7 +34560,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -24206,33 +34577,51 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24243,62 +34632,98 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_metabolite": { "description": "indicates whether a molecular entity is a metabolite", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24324,22 +34749,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24350,46 +34787,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24415,26 +34876,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24445,46 +34921,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24511,29 +35011,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24541,44 +35059,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24604,22 +35146,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -24627,14 +35181,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24642,38 +35202,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24700,22 +35278,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -24723,14 +35313,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24738,38 +35334,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24796,25 +35410,40 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_taxonomic_rank": { - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24822,38 +35451,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -24869,7 +35516,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -24880,11 +35530,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "associated_environmental_context": { "description": "the environment in which the two taxa interact", - "type": "string" + "type": [ + "string", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -24894,36 +35550,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -24931,7 +35605,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -24939,15 +35616,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the taxon that is the subject of the association", @@ -24955,48 +35641,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -25004,32 +35717,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the taxon that is the subject of the association", @@ -25037,44 +35765,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -25094,7 +35843,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25105,7 +35857,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25115,36 +35870,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25152,7 +35925,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25160,15 +35936,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the more general taxon", @@ -25176,48 +35961,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -25225,32 +36037,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the more specific taxon", @@ -25258,44 +36085,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -25315,7 +36163,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25326,7 +36177,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25336,36 +36190,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25373,7 +36245,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25381,15 +36256,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "An association between two individual organisms.", @@ -25397,48 +36281,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -25446,32 +36357,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -25479,44 +36405,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -25536,7 +36483,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25547,7 +36497,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25557,40 +36510,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25598,7 +36572,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25606,15 +36583,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -25622,25 +36608,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -25651,27 +36649,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -25679,36 +36695,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease.", @@ -25716,25 +36750,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -25745,23 +36791,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -25781,7 +36839,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -25792,7 +36853,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -25802,36 +36866,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -25839,7 +36921,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -25847,15 +36932,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -25863,48 +36957,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "interaction relationship type", @@ -25912,32 +37033,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -25945,44 +37081,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26002,7 +37159,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -26013,7 +37173,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -26023,47 +37186,71 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "identifier for the interaction. This may come from an interaction database such as IMEX.", "type": "string" }, "interacting_molecules_category": { - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -26071,15 +37258,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.", @@ -26087,48 +37283,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "interaction relationship type", @@ -26136,32 +37359,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.", @@ -26169,44 +37407,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26229,7 +37488,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -26244,29 +37506,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -26274,42 +37554,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -26319,31 +37620,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26370,22 +37686,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -26393,14 +37721,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26408,43 +37742,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26477,22 +37832,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26503,46 +37870,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26568,43 +37959,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26615,46 +38027,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26680,22 +38116,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -26703,14 +38151,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26718,43 +38172,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26787,43 +38262,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26834,46 +38330,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26909,22 +38429,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -26932,38 +38464,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -26989,22 +38539,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27015,46 +38577,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27070,7 +38656,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -27081,7 +38670,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -27091,55 +38683,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27147,7 +38772,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -27155,15 +38783,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -27171,25 +38808,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27200,27 +38849,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -27228,40 +38895,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -27269,25 +38957,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27298,23 +38998,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27334,7 +39046,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -27345,7 +39060,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -27355,55 +39073,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27411,7 +39162,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -27419,15 +39173,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -27435,25 +39198,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27464,27 +39239,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -27492,40 +39285,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -27533,25 +39347,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -27562,23 +39388,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27608,22 +39446,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -27631,14 +39481,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27646,38 +39502,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27704,22 +39578,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -27727,14 +39613,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27742,38 +39634,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27800,22 +39710,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27823,38 +39745,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27880,43 +39820,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "enabled_by": { "description": "holds between a process and a physical entity, where the physical entity executes the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_input": { "description": "holds between a process and a continuant, where the continuant is an input into the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_output": { "description": "holds between a process and a continuant, where the continuant is an output of the process", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -27927,46 +39888,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -27992,22 +39977,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28015,38 +40012,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28072,22 +40087,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28098,46 +40125,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28163,22 +40214,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28189,46 +40252,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28254,22 +40341,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28280,46 +40379,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28335,7 +40458,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -28346,7 +40472,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -28356,36 +40485,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28393,7 +40540,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -28401,15 +40551,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the population that form the object of the association", @@ -28417,48 +40576,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used", @@ -28466,32 +40652,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "the population that form the subject of the association", @@ -28499,44 +40700,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28566,22 +40788,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28592,46 +40826,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28647,14 +40905,20 @@ "properties": { "anatomical_context_qualifier": { "description": "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location).", - "type": "string" + "type": [ + "string", + "null" + ] }, "broad_match": { "description": "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "causal_mechanism_qualifier": { "$ref": "#/$defs/CausalMechanismQualifierEnum", @@ -28665,29 +40929,47 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "mapped_predicate": { "description": "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.", - "type": "string" + "type": [ + "string", + "null" + ] }, "narrow_match": { "description": "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "object_derivative_qualifier": { "description": "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier \u2018metabolite\u2019 combines with a \u2018Chemical X\u2019 core concept to express the composed concept \u2018a metabolite of Chemical X\u2019. This qualifier is for the object of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -28695,11 +40977,17 @@ }, "object_form_or_variant_qualifier": { "description": "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier \u2018mutation\u2019 combines with the core concept \u2018Gene X\u2019 to express the compose concept \u2018a mutation of Gene X\u2019. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_part_qualifier": { "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -28707,22 +40995,37 @@ }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "species_context_qualifier": { "description": "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_context_qualifier": { - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_derivative_qualifier": { "description": "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier \u2018metabolite\u2019 combines with a \u2018Chemical X\u2019 core concept to express the composed concept \u2018a metabolite of Chemical X\u2019. This qualifier is for the subject of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -28730,11 +41033,17 @@ }, "subject_form_or_variant_qualifier": { "description": "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier \u2018mutation\u2019 combines with the core concept \u2018Gene X\u2019 to express the compose concept \u2018a mutation of Gene X\u2019. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_part_qualifier": { "description": "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement).", - "type": "string" + "type": [ + "string", + "null" + ] } }, "required": [ @@ -28752,7 +41061,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -28767,29 +41079,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -28797,42 +41127,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -28842,31 +41193,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28893,22 +41259,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -28916,38 +41294,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -28963,7 +41359,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -28974,7 +41373,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -28984,36 +41386,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29021,7 +41441,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -29029,15 +41452,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -29045,48 +41477,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -29094,32 +41553,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -29127,44 +41601,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29187,7 +41682,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -29201,11 +41699,17 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "drug_regulatory_status_world_wide": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -29213,21 +41717,30 @@ }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "highest_FDA_approval_status": { "$ref": "#/$defs/ApprovalStatusEnum", @@ -29239,61 +41752,94 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_supplement": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "routes_of_delivery": { "description": "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.", "items": { "$ref": "#/$defs/DrugDeliveryEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29319,22 +41865,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29345,46 +41903,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29410,29 +41992,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29443,46 +42040,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29508,29 +42129,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_gene_or_gene_product": { "description": "connects an entity with one or more gene or gene products", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29541,46 +42177,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29606,22 +42266,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29632,46 +42304,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29690,7 +42386,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -29705,29 +42404,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -29735,42 +42452,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -29780,31 +42518,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29821,11 +42574,17 @@ "properties": { "has_numeric_value": { "description": "connects a quantity value to a number", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_unit": { "description": "connects a quantity value to a unit", - "type": "string" + "type": [ + "string", + "null" + ] } }, "title": "QuantityValue", @@ -29847,22 +42606,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29873,46 +42644,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -29938,22 +42733,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -29964,46 +42771,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30039,7 +42870,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -30050,7 +42884,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -30060,36 +42897,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30097,7 +42952,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -30105,15 +42963,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "$ref": "#/$defs/GeneOrGeneProduct", @@ -30121,48 +42988,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -30170,25 +43064,37 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "reaction_direction": { "$ref": "#/$defs/ReactionDirectionEnum", @@ -30203,11 +43109,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stoichiometry": { "description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "subject": { "description": "the chemical entity or entity that is an interactor", @@ -30215,44 +43127,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30272,7 +43205,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -30283,7 +43219,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -30293,36 +43232,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30330,7 +43287,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -30338,15 +43298,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the chemical element that is the target of the statement", @@ -30354,48 +43323,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -30403,25 +43399,37 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "reaction_direction": { "$ref": "#/$defs/ReactionDirectionEnum", @@ -30436,11 +43444,17 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stoichiometry": { "description": "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers.", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "subject": { "description": "the chemical entity or entity that is an interactor", @@ -30448,44 +43462,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30515,26 +43550,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30545,46 +43595,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30610,26 +43684,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30640,46 +43729,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30721,29 +43834,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30751,44 +43882,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30839,29 +43994,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30869,21 +44042,33 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "resource_id": { "description": "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.", @@ -30894,31 +44079,46 @@ "description": "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "upstream_resource_ids": { "description": "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -30936,7 +44136,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -30947,7 +44150,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -30957,36 +44163,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -30994,7 +44218,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -31002,15 +44229,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -31018,48 +44254,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -31067,32 +44330,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -31100,44 +44378,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31166,7 +44465,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -31177,7 +44479,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -31187,36 +44492,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31224,7 +44547,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -31232,15 +44558,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -31248,48 +44583,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -31297,32 +44659,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -31330,44 +44707,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31397,33 +44795,51 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "The state of the sequence w.r.t a reference sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_gene": { "description": "Each allele can be associated with any number of genes", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31434,46 +44850,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31492,7 +44932,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -31507,29 +44950,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Serials (journals) should have industry-standard identifier such as from ISSN.", @@ -31537,50 +44998,77 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iso_abbreviation": { "description": "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.", - "type": "string" + "type": [ + "string", + "null" + ] }, "issue": { "description": "issue of a newspaper, a scientific journal or magazine for reference purpose", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -31590,36 +45078,54 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "description": "Should generally be set to an ontology class defined term for 'serial' or 'journal'.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "volume": { "description": "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31646,22 +45152,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -31669,14 +45187,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31684,38 +45208,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31742,22 +45284,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31768,46 +45322,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31826,7 +45404,10 @@ "items": { "$ref": "#/$defs/DrugAvailabilityEnum" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -31840,29 +45421,44 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_chemical_role": { "description": "A role is particular behaviour which a chemical entity may exhibit.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31870,54 +45466,84 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "is_metabolite": { "description": "indicates whether a molecular entity is a metabolite", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "is_toxic": { "description": "", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "max_tolerated_dose": { "description": "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "trade_name": { "description": "", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -31943,33 +45569,51 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "The state of the sequence w.r.t a reference sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_gene": { "description": "Each allele can be associated with any number of genes", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -31980,46 +45624,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32045,22 +45713,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -32068,14 +45748,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32083,38 +45769,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32141,15 +45845,24 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", @@ -32164,14 +45877,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32179,43 +45898,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32260,22 +46000,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32283,38 +46035,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32340,22 +46110,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32366,46 +46148,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32432,29 +46238,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32462,44 +46286,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32515,7 +46363,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -32526,7 +46377,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -32536,36 +46390,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32573,7 +46445,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -32581,15 +46456,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "An association between individuals of different taxa.", @@ -32597,48 +46481,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -32646,32 +46557,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -32679,44 +46605,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32762,29 +46709,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32792,44 +46757,68 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32855,22 +46844,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32881,46 +46882,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -32936,7 +46961,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -32947,7 +46975,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -32957,36 +46988,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -32994,7 +47043,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -33002,15 +47054,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -33018,48 +47079,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -33067,32 +47155,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -33100,44 +47203,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33167,26 +47291,41 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_biological_sequence": { "description": "connects a genomic feature to its sequence", - "type": "string" + "type": [ + "string", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33197,46 +47336,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33262,43 +47425,64 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_device": { "description": "connects an entity to one or more (medical) devices", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_drug": { "description": "connects an entity to one or more drugs", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_procedure": { "description": "connects an entity to one or more (medical) procedures", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33306,43 +47490,64 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33358,7 +47563,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -33369,7 +47577,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33379,40 +47590,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33420,7 +47652,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -33428,15 +47663,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "disease", @@ -33444,25 +47688,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -33473,27 +47729,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "The relationship to the disease", @@ -33501,36 +47775,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "A variant that has a role in modeling the disease.", @@ -33538,25 +47830,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -33567,23 +47871,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33603,7 +47919,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -33614,7 +47933,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33624,40 +47946,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33665,7 +48008,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -33673,15 +48019,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "a disease that is associated with that variant", @@ -33689,25 +48044,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -33718,27 +48085,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "E.g. is pathogenic for", @@ -33746,36 +48131,54 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "a sequence variant in which the allele state is associated in some way with the disease state", @@ -33783,25 +48186,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -33812,23 +48227,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -33848,7 +48275,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -33859,7 +48289,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -33869,36 +48302,54 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -33906,7 +48357,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -33914,15 +48368,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -33930,48 +48393,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -33979,32 +48469,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "a sequence variant in which the allele state is associated with some other entity", @@ -34012,44 +48517,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34069,7 +48595,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -34080,7 +48609,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -34090,40 +48622,61 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "expression_site": { "description": "location in which gene or protein expression takes place. May be cell, tissue, or organ.", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34131,7 +48684,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -34139,15 +48695,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -34155,52 +48720,82 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "phenotypic_state": { "description": "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -34208,40 +48803,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "quantifier_qualifier": { "description": "Optional quantitative value indicating degree of expression.", - "type": "string" + "type": [ + "string", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "stage_qualifier": { "description": "stage during which gene or protein expression of takes place.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "a sequence variant in which the allele state is associated with some other entity", @@ -34249,44 +48865,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34306,7 +48943,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -34317,7 +48957,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -34327,55 +48970,88 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number of things with a particular property", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "total number of things in a particular reference set", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34383,7 +49059,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -34391,15 +49070,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.", @@ -34407,25 +49095,37 @@ }, "object_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -34436,27 +49136,45 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -34464,40 +49182,61 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualified_predicate": { "description": "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading.", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "sex_qualifier": { "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject": { "description": "a sequence variant in which the allele state is associated in some way with the phenotype state", @@ -34505,25 +49244,37 @@ }, "subject_aspect_qualifier": { "description": "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement).", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_direction_qualifier": { "$ref": "#/$defs/DirectionQualifierEnum", @@ -34534,23 +49285,35 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34570,7 +49333,10 @@ "properties": { "adjusted_p_value": { "description": "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<.", - "type": "number" + "type": [ + "number", + "null" + ] }, "agent_type": { "$ref": "#/$defs/AgentTypeEnum", @@ -34581,7 +49347,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -34591,56 +49360,89 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "frequency_qualifier": { "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_count": { "description": "number in object population that carry a particular allele, aka allele count", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "has_evidence": { "description": "connects an association to an instance of supporting evidence", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_percentage": { "description": "equivalent to has quotient multiplied by 100", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_quotient": { "description": "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency", - "type": "number" + "type": [ + "number", + "null" + ] }, "has_supporting_studies": { "description": "A study that produced information used as evidence to generate the knowledge expressed in an Association.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_total": { "description": "number all populations that carry a particular allele, aka allele number", - "type": "integer" + "type": [ + "integer", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34648,7 +49450,10 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "knowledge_level": { "$ref": "#/$defs/KnowledgeLevelEnum", @@ -34656,15 +49461,24 @@ }, "knowledge_source": { "description": "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "negated": { "description": "if set to true, then the association is negated i.e. is not true", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "object": { "description": "the population that is observed to have the frequency", @@ -34672,48 +49486,75 @@ }, "object_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "object_category_closure": { "description": "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_closure": { "description": "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_label_closure": { "description": "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "object_namespace": { "description": "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_object": { "description": "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_predicate": { "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "original_subject": { "description": "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification.", - "type": "string" + "type": [ + "string", + "null" + ] }, "p_value": { "description": "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.", - "type": "number" + "type": [ + "number", + "null" + ] }, "predicate": { "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.", @@ -34721,32 +49562,47 @@ }, "primary_knowledge_source": { "description": "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.", - "type": "string" + "type": [ + "string", + "null" + ] }, "publications": { "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "qualifier": { "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes", - "type": "string" + "type": [ + "string", + "null" + ] }, "qualifiers": { "description": "connects an association to qualifiers that modify or qualify the meaning of that association", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "retrieval_source_ids": { "description": "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject": { "description": "an allele that has a certain frequency in a given population", @@ -34754,44 +49610,65 @@ }, "subject_category": { "description": "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "subject_category_closure": { "description": "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_closure": { "description": "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_label_closure": { "description": "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "subject_namespace": { "description": "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX.", - "type": "string" + "type": [ + "string", + "null" + ] }, "timepoint": { "description": "a point in time", "format": "time", - "type": "string" + "type": [ + "string", + "null" + ] }, "type": { "description": "rdf:type of biolink:Association should be fixed at rdf:Statement", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34821,22 +49698,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34847,46 +49736,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34912,22 +49825,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "may often be an organism attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -34938,46 +49863,70 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "in_taxon_label": { "description": "The human readable scientific name for the taxon of the entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "A human-readable name for an attribute or entity.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -34996,7 +49945,10 @@ "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "category": { "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}", @@ -35011,29 +49963,47 @@ "creation_date": { "description": "date on which an entity was created. This can be applied to nodes or edges", "format": "date", - "type": "string" + "type": [ + "string", + "null" + ] }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "format": { - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.", @@ -35041,42 +50011,63 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "keywords": { "description": "keywords tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "license": { - "type": "string" + "type": [ + "string", + "null" + ] }, "mesh_terms": { "description": "mesh terms tagging a publication", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "name": { "description": "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).", - "type": "string" + "type": [ + "string", + "null" + ] }, "pages": { "description": "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "publication_type": { "description": "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.", @@ -35086,31 +50077,46 @@ "type": "array" }, "rights": { - "type": "string" + "type": [ + "string", + "null" + ] }, "summary": { "description": "executive summary of a publication", - "type": "string" + "type": [ + "string", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ @@ -35137,22 +50143,34 @@ }, "deprecated": { "description": "A boolean flag indicating that an entity is no longer considered current or valid.", - "type": "boolean" + "type": [ + "boolean", + "null" + ] }, "description": { "description": "a human-readable description of an entity", - "type": "string" + "type": [ + "string", + "null" + ] }, "full_name": { "description": "a long-form human readable name for a thing", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_attribute": { "description": "connects any entity to an attribute", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "has_attribute_type": { "description": "connects an attribute to a class that describes it", @@ -35160,14 +50178,20 @@ }, "has_qualitative_value": { "description": "connects an attribute to a value", - "type": "string" + "type": [ + "string", + "null" + ] }, "has_quantitative_value": { "description": "connects an attribute to a value", "items": { "$ref": "#/$defs/QuantityValue" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "id": { "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI", @@ -35175,38 +50199,56 @@ }, "iri": { "description": "An IRI for an entity. This is determined by the id using expansion rules.", - "type": "string" + "type": [ + "string", + "null" + ] }, "name": { "description": "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.", - "type": "string" + "type": [ + "string", + "null" + ] }, "provided_by": { "description": "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "synonym": { "description": "Alternate human-readable names for a thing", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "type": { "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] }, "xref": { "description": "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.", "items": { "type": "string" }, - "type": "array" + "type": [ + "array", + "null" + ] } }, "required": [ diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl index 17413a657..b0ce9da6e 100644 --- a/project/owl/biolink_model.owl.ttl +++ b/project/owl/biolink_model.owl.ttl @@ -123,10 +123,10 @@ biolink:HospitalizationOutcome a owl:Class ; biolink:MappingCollection a owl:Class ; rdfs:label "mapping collection" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:PredicateMapping ; owl:onProperty biolink:predicate_mappings ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PredicateMapping ; + owl:minCardinality 0 ; owl:onProperty biolink:predicate_mappings ], linkml:ClassDefinition ; skos:definition "A collection of deprecated mappings." ; @@ -2593,13 +2593,13 @@ biolink:AccessibleDnaRegion a owl:Class ; rdfs:label "accessible dna region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], @@ -2648,32 +2648,32 @@ biolink:AccessibleDnaRegion a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; skos:inScheme . @@ -2682,30 +2682,30 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; @@ -2797,8 +2797,17 @@ biolink:Bacterium a owl:Class ; biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Behavior ; owl:onProperty biolink:subject ], @@ -2808,15 +2817,6 @@ biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:BehavioralFeature ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; skos:inScheme . @@ -2844,17 +2844,17 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:type ], @@ -2872,10 +2872,10 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:CaseToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; skos:inScheme . @@ -2883,29 +2883,29 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:label "causal gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -2998,9 +2998,6 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; @@ -3009,6 +3006,9 @@ biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom biolink:CellLine ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], @@ -3024,65 +3024,77 @@ biolink:CellLineToEntityAssociationMixin a owl:Class ; biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_direction_qualifier ], @@ -3090,101 +3102,89 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme . @@ -3192,72 +3192,72 @@ biolink:ChemicalAffectsGeneAssociation a owl:Class ; biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "A regulatory relationship between two genes" ; @@ -3266,107 +3266,107 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], biolink:Association ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; skos:exactMatch SIO:001257 ; @@ -3375,17 +3375,17 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment side effect disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -3416,20 +3416,23 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:catalyst_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:catalyst_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], @@ -3437,14 +3440,11 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], @@ -3458,13 +3458,13 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -3477,26 +3477,26 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalToPathwayAssociation a owl:Class ; rdfs:label "chemical to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An interaction between a chemical entity and a biological process or pathway." ; skos:exactMatch SIO:001250 ; @@ -3614,62 +3614,62 @@ biolink:ContributorAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:allValuesFrom biolink:InformationContentEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - biolink:Association ; - skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; - skos:inScheme . + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + biolink:Association ; + skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; + skos:inScheme . biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; rdfs:label "correlated gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -3702,26 +3702,26 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneticInheritance ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneticInheritance ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; skos:inScheme . @@ -3748,10 +3748,10 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; rdfs:label "disease to exposure event association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ], + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ], biolink:Association ; skos:definition "An association between an exposure event and a disease." ; skos:inScheme . @@ -3759,41 +3759,41 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], + owl:allValuesFrom biolink:Onset ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:onset_qualifier ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], biolink:Association ; skos:closeMatch dcid:DiseaseSymptomAssociation ; skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; @@ -3845,17 +3845,17 @@ biolink:DrugToEntityAssociationMixin a owl:Class ; biolink:DrugToGeneAssociation a owl:Class ; rdfs:label "drug to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a drug and a gene or gene product." ; skos:inScheme ; @@ -3893,35 +3893,35 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; + owl:onProperty biolink:has_evidence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3929,13 +3929,13 @@ biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_approval_status ], + owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], @@ -3944,7 +3944,7 @@ biolink:EntityToDiseaseAssociation a owl:Class ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:max_research_phase ], + owl:onProperty biolink:clinical_approval_status ], biolink:Association ; skos:inScheme . @@ -3963,23 +3963,23 @@ biolink:EntityToOutcomeAssociationMixin a owl:Class ; biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "entity to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ResearchPhaseEnum ; - owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:clinical_approval_status ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ResearchPhaseEnum ; + owl:onProperty biolink:max_research_phase ], biolink:Association ; skos:inScheme . @@ -4020,10 +4020,7 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Transcript ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -4035,7 +4032,10 @@ biolink:ExonToTranscriptRelationship a owl:Class ; owl:allValuesFrom biolink:Exon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Transcript ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:SequenceFeatureRelationship ; skos:definition "A transcript is formed from multiple exons" ; @@ -4044,25 +4044,25 @@ biolink:ExonToTranscriptRelationship a owl:Class ; biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:temporal_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:minCardinality 0 ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:time ; owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:population_context_qualifier ], biolink:Association ; skos:definition "An association between an exposure event and an outcome." ; @@ -4076,12 +4076,12 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; skos:inScheme . @@ -4139,175 +4139,175 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; rdfs:label "gene affects chemical association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], biolink:Association ; skos:definition "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; skos:inScheme . @@ -4315,17 +4315,17 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "gene as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -4336,7 +4336,10 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -4344,32 +4347,29 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -4656,68 +4656,68 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; biolink:GeneRegulatesGeneAssociation a owl:Class ; rdfs:label "gene regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:species_context_qualifier ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . @@ -4726,50 +4726,50 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:quantifier_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:LifeStage ; owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" ; @@ -4778,17 +4778,17 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; skos:inScheme . @@ -4799,28 +4799,28 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneFamily ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; @@ -4829,20 +4829,20 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], @@ -4851,10 +4851,10 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:GeneToGeneAssociation ; skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; skos:inScheme . @@ -4863,30 +4863,30 @@ biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneProductMixin ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; @@ -4898,17 +4898,17 @@ biolink:GeneToGoTermAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], @@ -4922,6 +4922,12 @@ biolink:GeneToPathwayAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -4931,15 +4937,9 @@ biolink:GeneToPathwayAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], biolink:Association ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; skos:inScheme . @@ -4948,12 +4948,12 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:PhenotypicFeature ; @@ -4966,9 +4966,9 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:exactMatch WBVocab:Gene-Phenotype-Association ; @@ -4977,14 +4977,14 @@ biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; biolink:Genome a owl:Class ; rdfs:label "genome" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:closeMatch dcid:GenomeAssemblyUnit ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; @@ -4996,9 +4996,6 @@ biolink:Genome a owl:Class ; biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; @@ -5009,10 +5006,13 @@ biolink:GenomicBackgroundExposure a owl:Class ; owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ThingWithTaxon ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent ], biolink:Attribute ; skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; skos:inScheme . @@ -5020,13 +5020,10 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -5034,38 +5031,41 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:GenotypeToDiseaseAssociation ; skos:inScheme . biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; skos:inScheme . @@ -5073,17 +5073,14 @@ biolink:GenotypeToGeneAssociation a owl:Class ; biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -5091,14 +5088,17 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ; skos:inScheme . @@ -5106,11 +5106,8 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -5118,17 +5115,20 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; skos:inScheme . @@ -5136,32 +5136,32 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." ; skos:inScheme . @@ -5200,10 +5200,10 @@ biolink:GeographicExposure a owl:Class ; biolink:GeographicLocationAtTime a owl:Class ; rdfs:label "geographic location at time" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; + owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:time ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -5227,14 +5227,14 @@ biolink:GrossAnatomicalStructure a owl:Class ; biolink:Haplotype a owl:Class ; rdfs:label "haplotype" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:definition "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; skos:exactMatch , @@ -5265,29 +5265,29 @@ biolink:Human a owl:Class ; biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:label "information content entity to named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -5369,16 +5369,16 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:label "macromolecular machine to biological process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalProcess ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; @@ -5387,9 +5387,6 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; rdfs:label "macromolecular machine to cellular component association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], - [ a owl:Restriction ; owl:allValuesFrom biolink:CellularComponent ; owl:onProperty biolink:object ], [ a owl:Restriction ; @@ -5398,6 +5395,9 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; skos:inScheme . @@ -5405,11 +5405,11 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; rdfs:label "macromolecular machine to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -5423,32 +5423,32 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MaterialSample ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." ; skos:inScheme . @@ -5482,22 +5482,22 @@ biolink:MicroRNA a owl:Class ; biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; @@ -5506,22 +5506,22 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularActivity ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; @@ -5530,31 +5530,31 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularActivity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; @@ -5563,29 +5563,32 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ; biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], @@ -5593,35 +5596,32 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -5629,11 +5629,11 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], biolink:Association ; skos:inScheme . @@ -5651,10 +5651,10 @@ biolink:NucleosomeModification a owl:Class ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin ], + owl:someValuesFrom biolink:EpigenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity ], + owl:someValuesFrom biolink:GeneProductIsoformMixin ], biolink:BiologicalEntity ; skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; skos:inScheme . @@ -5668,76 +5668,76 @@ biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:associated_environmental_context ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:associated_environmental_context ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; skos:inScheme . @@ -5745,32 +5745,32 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; skos:inScheme . @@ -5778,72 +5778,63 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; biolink:OrganismToOrganismAssociation a owl:Class ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:IndividualOrganism ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:IndividualOrganism ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:IndividualOrganism ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:IndividualOrganism ; - owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:Association ; skos:inScheme . biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:object ], @@ -5851,20 +5842,29 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:interacting_molecules_category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:interacting_molecules_category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:interacting_molecules_category ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; skos:inScheme . @@ -5956,20 +5956,20 @@ biolink:Phenomenon a owl:Class ; biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; rdfs:label "phenotypic feature to disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], biolink:Association ; skos:inScheme . @@ -5977,10 +5977,10 @@ biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "phenotypic feature to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; skos:inScheme . @@ -6027,32 +6027,32 @@ biolink:Plant a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a two populations" ; skos:inScheme . @@ -6069,194 +6069,194 @@ biolink:PosttranslationalModification a owl:Class ; biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:broad_match ], + [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:narrow_match ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:exact_match ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:mapped_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:exact_match ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:mapped_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:broad_match ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:object_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:mapped_predicate ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:narrow_match ], linkml:ClassDefinition ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; skos:inScheme . @@ -6272,32 +6272,32 @@ biolink:PreprintPublication a owl:Class ; biolink:ProcessRegulatesProcessAssociation a owl:Class ; rdfs:label "process regulates process association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . @@ -6313,10 +6313,10 @@ biolink:ProteinDomain a owl:Class ; rdfs:label "protein domain" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:BiologicalEntity ; skos:definition "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; skos:exactMatch , @@ -6328,10 +6328,10 @@ biolink:ProteinFamily a owl:Class ; rdfs:label "protein family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], biolink:BiologicalEntity ; skos:exactMatch , WIKIDATA:Q2278983 ; @@ -6392,13 +6392,13 @@ biolink:RNAProductIsoform a owl:Class ; biolink:ReactionToCatalystAssociation a owl:Class ; rdfs:label "reaction to catalyst association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:ReactionToParticipantAssociation ; skos:inScheme . @@ -6410,10 +6410,10 @@ biolink:ReagentTargetedGene a owl:Class ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:altLabel "sequence targeting reagent" ; skos:definition "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; @@ -6490,23 +6490,23 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Treatment ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Treatment ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:inScheme ; @@ -6515,47 +6515,47 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iso_abbreviation ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:issue ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:volume ], biolink:Publication ; skos:altLabel "journal" ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; @@ -6607,10 +6607,10 @@ biolink:SocioeconomicExposure a owl:Class ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:SocioeconomicAttribute ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom biolink:SocioeconomicAttribute ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute ], biolink:Attribute ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; @@ -6653,23 +6653,23 @@ biolink:StudyVariable a owl:Class ; biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . @@ -6689,23 +6689,23 @@ biolink:TextMiningResult a owl:Class ; biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is a collection of transcripts" ; skos:inScheme . @@ -6717,13 +6717,13 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:RegulatoryRegion ; skos:altLabel "binding site", "tf binding site" ; @@ -6736,34 +6736,34 @@ biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:VariantToDiseaseAssociation ; skos:inScheme . biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" ; @@ -6772,42 +6772,39 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ; biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], biolink:Association ; skos:inScheme . biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; @@ -6816,35 +6813,38 @@ biolink:VariantToPopulationAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQualifierMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_total ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_quotient ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], biolink:Association ; skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ; skos:inScheme . @@ -7423,41 +7423,41 @@ biolink:AdministrativeEntity a owl:Class ; biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:issue ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], + owl:minCardinality 1 ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:maxCardinality 1 ; + owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:published_in ], + owl:minCardinality 0 ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:issue ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:published_in ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; skos:exactMatch fabio:article, @@ -7468,10 +7468,10 @@ biolink:Behavior a owl:Class ; rdfs:label "behavior" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ActivityAndBehavior ], biolink:BiologicalProcess ; skos:exactMatch STY:T053, ; @@ -7490,32 +7490,32 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:minCardinality 0 ; + owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty biolink:chapter ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:chapter ], + owl:maxCardinality 1 ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:chapter ], biolink:Publication ; skos:inScheme . @@ -7533,20 +7533,20 @@ biolink:Case a owl:Class ; biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "cell line to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; skos:inScheme . @@ -7568,12 +7568,12 @@ biolink:ChemicalExposure a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_quantitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], biolink:Attribute ; skos:definition "A chemical exposure is an intake of a particular chemical entity." ; skos:exactMatch ECTO:9000000, @@ -7583,29 +7583,29 @@ biolink:ChemicalExposure a owl:Class ; biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:FDA_adverse_event_level ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; - owl:onProperty biolink:FDA_adverse_event_level ], biolink:Association ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; skos:inScheme . @@ -7722,10 +7722,10 @@ biolink:GeneFamily a owl:Class ; rdfs:label "gene family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; skos:altLabel "orthogroup", "protein family" ; @@ -7741,76 +7741,76 @@ biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phase ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:allValuesFrom biolink:PhaseEnum ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:genome_build ], + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:genome_build ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhaseEnum ; - owl:onProperty biolink:phase ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:end_interbase_coordinate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:genome_build ], + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:minCardinality 0 ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:strand ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:phase ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:start_interbase_coordinate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:StrandEnum ; owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:genome_build ], biolink:SequenceAssociation ; skos:broadMatch dcid:Chromosome ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; @@ -7820,38 +7820,38 @@ biolink:GenomicSequenceLocalization a owl:Class ; biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7864,23 +7864,23 @@ biolink:GenotypeToEntityAssociationMixin a owl:Class ; biolink:GeographicLocation a owl:Class ; rdfs:label "geographic location" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:longitude ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:longitude ], + owl:onProperty biolink:latitude ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:latitude ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; + owl:maxCardinality 1 ; owl:onProperty biolink:longitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:latitude ], + owl:onProperty biolink:longitude ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:longitude ], biolink:PlanetaryEntity ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch STY:T083, @@ -7925,10 +7925,10 @@ biolink:PairwiseGeneToGeneInteraction a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; @@ -7947,10 +7947,10 @@ biolink:Polypeptide a owl:Class ; rdfs:label "polypeptide" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], biolink:BiologicalEntity ; skos:altLabel "amino acid entity" ; skos:definition "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; @@ -7962,41 +7962,41 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:reaction_direction ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:allValuesFrom biolink:ReactionDirectionEnum ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stoichiometry ], + owl:allValuesFrom biolink:ReactionSideEnum ; + owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:stoichiometry ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ReactionSideEnum ; - owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_side ], + owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:integer ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_direction ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:reaction_side ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:ChemicalToChemicalAssociation ; skos:inScheme . @@ -8028,29 +8028,29 @@ biolink:StudyPopulation a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:Device ; + owl:onProperty biolink:has_device ], + [ a owl:Restriction ; owl:allValuesFrom biolink:Procedure ; owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_drug ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Device ; - owl:onProperty biolink:has_device ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:has_drug ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_device ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_procedure ], biolink:NamedThing ; skos:altLabel "medical action", "medical intervention" ; @@ -8063,38 +8063,38 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -8102,15 +8102,6 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; @@ -8122,6 +8113,15 @@ biolink:VariantToGeneAssociation a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], biolink:Association ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; skos:inScheme . @@ -8779,22 +8779,22 @@ biolink:ActivityAndBehavior a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . @@ -8827,35 +8827,35 @@ biolink:ChemicalRole a owl:Class ; biolink:ChemicalToChemicalAssociation a owl:Class ; rdfs:label "chemical to chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; skos:inScheme . @@ -8932,26 +8932,20 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -8959,29 +8953,35 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme ; skos:narrowMatch WBVocab:Gene-Phenotype-Association, @@ -9037,26 +9037,26 @@ biolink:Onset a owl:Class ; biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "A relationship between two organism taxon nodes" ; skos:inScheme . @@ -9104,16 +9104,16 @@ biolink:RegulatoryRegion a owl:Class ; rdfs:label "regulatory region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:altLabel "regulatory element" ; skos:definition "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; @@ -9464,13 +9464,13 @@ biolink:CellularComponent a owl:Class ; biolink:DatasetDistribution a owl:Class ; rdfs:label "dataset distribution" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:distribution_download_url ], biolink:InformationContentEntity ; skos:definition "an item that holds distribution level information about a dataset." ; @@ -9480,11 +9480,11 @@ biolink:DatasetDistribution a owl:Class ; biolink:DatasetSummary a owl:Class ; rdfs:label "dataset summary" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:source_web_page ], + owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_web_page ], @@ -9492,10 +9492,10 @@ biolink:DatasetSummary a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:source_logo ], + owl:minCardinality 0 ; + owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_logo ], biolink:InformationContentEntity ; skos:definition "an item that holds summary level information about a dataset." ; @@ -9530,10 +9530,10 @@ biolink:GeneToGeneAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -9622,21 +9622,21 @@ biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_numeric_value ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_unit ], + owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty biolink:has_unit ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_numeric_value ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_numeric_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:has_unit ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; @@ -9652,6 +9652,12 @@ biolink:ResourceRoleEnum a owl:Class ; biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; @@ -9659,16 +9665,10 @@ biolink:SequenceFeatureRelationship a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:object ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; skos:exactMatch CHADO:feature_relationship ; @@ -9792,26 +9792,26 @@ biolink:DatasetVersion a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:ingest_date ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Dataset ; - owl:onProperty biolink:has_dataset ], + owl:allValuesFrom biolink:DatasetDistribution ; + owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:ingest_date ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DatasetDistribution ; - owl:onProperty biolink:has_distribution ], + owl:allValuesFrom biolink:Dataset ; + owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_dataset ], @@ -9843,13 +9843,13 @@ biolink:FDAIDAAdverseEventEnum a owl:Class ; biolink:FunctionalAssociation a owl:Class ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -9858,7 +9858,7 @@ biolink:FunctionalAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; @@ -10247,14 +10247,14 @@ biolink:CellularOrganism a owl:Class ; biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:highest_FDA_approval_status ], @@ -10262,23 +10262,23 @@ biolink:ChemicalMixture a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ApprovalStatusEnum ; owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ApprovalStatusEnum ; + owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:routes_of_delivery ], [ a owl:Restriction ; owl:allValuesFrom biolink:DrugDeliveryEnum ; owl:onProperty biolink:routes_of_delivery ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; - owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:is_supplement ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:drug_regulatory_status_world_wide ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -10306,27 +10306,27 @@ biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:closeMatch dcid:DiseaseGeneAssociation ; skos:exactMatch SIO:000983 ; @@ -10342,38 +10342,38 @@ biolink:MacromolecularMachineMixin a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:enabled_by ], + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_output ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], biolink:BiologicalProcessOrActivity ; skos:altLabel "molecular event", "molecular function", @@ -10393,38 +10393,38 @@ biolink:PhysicalEssenceOrOccurrent a owl:Class ; biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:allValuesFrom biolink:ResourceRoleEnum ; + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:resource_id ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ResourceRoleEnum ; owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:upstream_resource_ids ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:resource_role ], + owl:onProperty biolink:resource_id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:upstream_resource_ids ], biolink:InformationContentEntity ; skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; skos:inScheme . @@ -10768,10 +10768,10 @@ biolink:Drug a owl:Class ; rdfs:label "drug" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], + owl:someValuesFrom biolink:OntologyClass ], biolink:MolecularMixture ; skos:broadMatch STY:T121 ; skos:definition "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; @@ -10787,16 +10787,16 @@ biolink:Genotype a owl:Class ; rdfs:label "genotype" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Zygosity ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Zygosity ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_zygosity ], @@ -10896,26 +10896,11 @@ biolink:AgentTypeEnum a owl:Class ; biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:deprecated ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Attribute ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:deprecated ], + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:name ], @@ -10923,41 +10908,56 @@ biolink:Entity a owl:Class ; owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:description ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:description ], + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:description ], + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:minCardinality 0 ; owl:onProperty biolink:category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iri ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:description ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:description ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:deprecated ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:description ], linkml:ClassDefinition ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; skos:inScheme . @@ -11038,16 +11038,16 @@ biolink:NucleicAcidEntity a owl:Class ; rdfs:label "nucleic acid entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:MolecularEntity ; skos:altLabel "genomic entity", "sequence feature" ; @@ -11060,14 +11060,14 @@ biolink:NucleicAcidEntity a owl:Class ; biolink:OrganismalEntity a owl:Class ; rdfs:label "organismal entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:has_attribute ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:has_attribute ], biolink:BiologicalEntity ; skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; skos:exactMatch , @@ -11175,38 +11175,38 @@ biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:has_output ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:PhysicalEntity ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhysicalEntity ; - owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:minCardinality 0 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:has_output ], + owl:onProperty biolink:has_input ], biolink:BiologicalEntity ; skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; skos:inScheme . @@ -11214,38 +11214,38 @@ biolink:BiologicalProcessOrActivity a owl:Class ; biolink:Agent a owl:Class ; rdfs:label "agent" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:address ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:affiliation ], + owl:maxCardinality 1 ; + owl:onProperty biolink:address ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:address ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:address ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:affiliation ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -11361,14 +11361,14 @@ biolink:DirectionQualifierEnum a owl:Class ; biolink:MolecularEntity a owl:Class ; rdfs:label "molecular entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:is_metabolite ], - [ a owl:Restriction ; owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:is_metabolite ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:is_metabolite ], biolink:ChemicalEntity ; skos:definition "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; skos:inScheme ; @@ -11383,10 +11383,10 @@ biolink:OrganismTaxon a owl:Class ; owl:allValuesFrom biolink:TaxonomicRank ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_taxonomic_rank ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:has_taxonomic_rank ], biolink:NamedThing ; skos:altLabel "taxon", @@ -11417,41 +11417,41 @@ biolink:BiologicalProcess a owl:Class ; biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:format ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; - owl:onProperty biolink:creation_date ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:format ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:license ], + owl:maxCardinality 1 ; + owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:format ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:date ; owl:onProperty biolink:creation_date ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:creation_date ], + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:format ], + owl:onProperty biolink:creation_date ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -11509,50 +11509,50 @@ biolink:CausalMechanismQualifierEnum a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:QuantityValue ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iri ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_qualitative_value ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_qualitative_value ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:has_qualitative_value ], + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_attribute_type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], biolink:NamedThing ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; skos:exactMatch SIO:000614 ; @@ -11577,35 +11577,35 @@ biolink:object_direction_qualifier a owl:ObjectProperty ; biolink:Gene a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:symbol ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:symbol ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], biolink:BiologicalEntity ; skos:broadMatch ; skos:definition "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; @@ -11619,38 +11619,38 @@ biolink:Gene a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], biolink:BiologicalEntity ; skos:altLabel "allele" ; skos:closeMatch , @@ -11694,68 +11694,68 @@ biolink:AnatomicalEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:summary ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:mesh_terms ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:authors ], + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:keywords ], + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:publication_type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:authors ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:pages ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:minCardinality 0 ; + owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:keywords ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:keywords ], + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:publication_type ], + owl:onProperty biolink:keywords ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:pages ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:mesh_terms ], + owl:onProperty biolink:summary ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:authors ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:pages ], biolink:InformationContentEntity ; skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; skos:exactMatch IAO:0000311 ; @@ -11779,7 +11779,10 @@ biolink:BiologicalEntity a owl:Class ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -11789,46 +11792,43 @@ biolink:ChemicalEntity a owl:Class ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:max_tolerated_dose ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:available_from ], + owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_chemical_role ], + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:is_toxic ], + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:is_toxic ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalRole ; owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:trade_name ], + owl:minCardinality 0 ; + owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; - owl:onProperty biolink:available_from ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:max_tolerated_dose ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:is_toxic ], biolink:NamedThing ; skos:broadMatch STY:T167 ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -11967,260 +11967,260 @@ biolink:association_slot a owl:DatatypeProperty ; biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:minCardinality 0 ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:publications ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:p_value ], + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:p_value ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:agent_type ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Study ; + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:original_predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_closure ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_closure ], + owl:minCardinality 0 ; + owl:onProperty biolink:original_object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:negated ], + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:original_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_namespace ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_label_closure ], + owl:maxCardinality 1 ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_object ], + owl:minCardinality 0 ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_category_closure ], + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ], + owl:minCardinality 0 ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:retrieval_source_ids ], + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:agent_type ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_label_closure ], + owl:onProperty biolink:subject_closure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:onProperty biolink:retrieval_source_ids ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AgentTypeEnum ; - owl:onProperty biolink:agent_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], + owl:minCardinality 0 ; + owl:onProperty biolink:knowledge_source ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:object_closure ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:time ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_closure ], + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:adjusted_p_value ], + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_label_closure ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_closure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AgentTypeEnum ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:allValuesFrom biolink:KnowledgeLevelEnum ; owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_supporting_studies ], + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:object_category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:maxCardinality 1 ; + owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_namespace ], + owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:p_value ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:adjusted_p_value ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_category ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_category ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:knowledge_source ], + owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:subject_category_closure ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_label_closure ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_closure ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_level ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_category_closure ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:negated ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_namespace ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_namespace ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_namespace ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_closure ], + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Study ; - owl:onProperty biolink:has_supporting_studies ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualifier ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -12240,38 +12240,38 @@ biolink:related_to_at_instance_level a owl:DatatypeProperty, biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:full_name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:full_name ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:category ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:full_name ], + owl:onProperty biolink:provided_by ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:provided_by ], + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], + owl:onProperty biolink:provided_by ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:category ], + owl:onProperty biolink:full_name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:synonym ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:provided_by ], + owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:category ], biolink:Entity ; skos:definition "a databased entity or concept/class" ; skos:exactMatch STY:T071, @@ -12324,32 +12324,80 @@ biolink:subject a owl:ObjectProperty ; skos:inScheme . [] a owl:Restriction ; - rdfs:subClassOf biolink:WebPage ; + rdfs:subClassOf biolink:PhenotypicQuality ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:WebPage . + owl:someValuesFrom biolink:PhenotypicQuality . [] a owl:Restriction ; - rdfs:subClassOf biolink:Book ; + rdfs:subClassOf biolink:SeverityValue ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Book . + owl:someValuesFrom biolink:SeverityValue . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicSequenceLocalization ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicSequenceLocalization . + owl:someValuesFrom biolink:GeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinFamily ; + rdfs:subClassOf biolink:ReactionToCatalystAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinFamily . + owl:someValuesFrom biolink:ReactionToCatalystAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Entity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Entity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ProteinDomain ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ProteinDomain . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EnvironmentalProcess ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EnvironmentalProcess . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BehavioralExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BehavioralExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GrossAnatomicalStructure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GrossAnatomicalStructure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SequenceVariant ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SequenceVariant . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:frequency_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -12357,223 +12405,270 @@ biolink:subject a owl:ObjectProperty ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin . + owl:someValuesFrom biolink:FrequencyQualifierMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:LifeStage ; + rdfs:subClassOf biolink:MaterialSample ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LifeStage . + owl:someValuesFrom biolink:MaterialSample . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicQuality ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicQuality . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Case ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Hospitalization ; + rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Hospitalization . + owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceAssociation ; + rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceAssociation . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalProcess ; + rdfs:subClassOf biolink:Phenomenon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalProcess . + owl:someValuesFrom biolink:Phenomenon . [] a owl:Restriction ; - rdfs:subClassOf biolink:Drug ; + rdfs:subClassOf biolink:Case ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Drug . + owl:someValuesFrom biolink:Case . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicExposure ; + rdfs:subClassOf biolink:GeneticInheritance ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicExposure . + owl:someValuesFrom biolink:GeneticInheritance . [] a owl:Restriction ; - rdfs:subClassOf biolink:TextMiningResult ; + rdfs:subClassOf biolink:Vertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TextMiningResult . + owl:someValuesFrom biolink:Vertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalTrial ; + rdfs:subClassOf biolink:Study ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalTrial . + owl:someValuesFrom biolink:Study . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + rdfs:subClassOf biolink:FoodAdditive ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToCatalystAssociation . + owl:someValuesFrom biolink:FoodAdditive . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocationAtTime ; + rdfs:subClassOf biolink:GenomicSequenceLocalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocationAtTime . + owl:someValuesFrom biolink:GenomicSequenceLocalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; + rdfs:subClassOf biolink:DrugToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . + owl:someValuesFrom biolink:DrugToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; + rdfs:subClassOf biolink:Cell ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceFeatureRelationship . + owl:someValuesFrom biolink:Cell . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ChiSquaredAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:Entity ; + rdfs:subClassOf biolink:ClinicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Entity . + owl:someValuesFrom biolink:ClinicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; + rdfs:subClassOf biolink:Dataset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . + owl:someValuesFrom biolink:Dataset . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariant ; + rdfs:subClassOf biolink:FunctionalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariant . + owl:someValuesFrom biolink:FunctionalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; + rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivity . + owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxon ; + rdfs:subClassOf biolink:SmallMolecule ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxon . + owl:someValuesFrom biolink:SmallMolecule . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom biolink:Outcome ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . + owl:someValuesFrom biolink:GenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Behavior ; + rdfs:subClassOf biolink:MolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Behavior . + owl:someValuesFrom biolink:MolecularMixture . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:frequency_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:frequency_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeature ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeature . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneProductRelationship ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneProductRelationship . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:RetrievalSource ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RetrievalSource . + owl:someValuesFrom biolink:GeneToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Patent ; + rdfs:subClassOf biolink:Protein ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Patent . + owl:someValuesFrom biolink:Protein . [] a owl:Restriction ; rdfs:subClassOf biolink:ProcessedMaterial ; @@ -12581,237 +12676,189 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:ProcessedMaterial . [] a owl:Restriction ; - rdfs:subClassOf biolink:Treatment ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Treatment . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; + rdfs:subClassOf biolink:Association ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToDiseaseAssociation . + owl:someValuesFrom biolink:Association . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalStructure . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; + rdfs:subClassOf biolink:Invertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + owl:someValuesFrom biolink:Invertebrate . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalIntervention ; + rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalIntervention . + owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Serial ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Serial . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SpecificityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyResult ; + rdfs:subClassOf biolink:GenomicBackgroundExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyResult . + owl:someValuesFrom biolink:GenomicBackgroundExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Plant ; + rdfs:subClassOf biolink:MolecularActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Plant . + owl:someValuesFrom biolink:MolecularActivity . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptToGeneRelationship ; + rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptToGeneRelationship . + owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; + rdfs:subClassOf biolink:RegulatoryRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . + owl:someValuesFrom biolink:RegulatoryRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; + rdfs:subClassOf biolink:NamedThing ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + owl:someValuesFrom biolink:NamedThing . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalFinding ; + rdfs:subClassOf biolink:ConfidenceLevel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalFinding . + owl:someValuesFrom biolink:ConfidenceLevel . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + rdfs:subClassOf biolink:VariantToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + owl:someValuesFrom biolink:VariantToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + rdfs:subClassOf biolink:PlanetaryEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . + owl:someValuesFrom biolink:PlanetaryEntity . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Human ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Human . + owl:someValuesFrom biolink:EpigenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + rdfs:subClassOf biolink:TaxonToTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismToOrganismAssociation . + owl:someValuesFrom biolink:TaxonToTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:Plant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:Plant . [] a owl:Restriction ; - rdfs:subClassOf biolink:Fungus ; + rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Fungus . + owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; + rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularEntity ; + rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularEntity . + owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon ], + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon ], + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ] ; + owl:onProperty biolink:timepoint ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon . + owl:someValuesFrom biolink:ExposureEvent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Dataset ; + rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Dataset . + owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugExposure ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugExposure . + owl:someValuesFrom biolink:ReactionToParticipantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; + rdfs:subClassOf biolink:TextMiningResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . + owl:someValuesFrom biolink:TextMiningResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProductIsoform ; + rdfs:subClassOf biolink:PhysiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProductIsoform . + owl:someValuesFrom biolink:PhysiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineMixin . + rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; + rdfs:subClassOf biolink:ConceptCountAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalExposure . + owl:someValuesFrom biolink:ConceptCountAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:FoodAdditive ; + rdfs:subClassOf biolink:Device ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FoodAdditive . + owl:someValuesFrom biolink:Device . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Bacterium ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Bacterium . [] a owl:Restriction ; rdfs:subClassOf biolink:ClinicalAttribute ; @@ -12819,97 +12866,127 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:ClinicalAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + rdfs:subClassOf biolink:PopulationToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseAssociation . + owl:someValuesFrom biolink:PopulationToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleosomeModification ; + rdfs:subClassOf biolink:Article ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleosomeModification . + owl:someValuesFrom biolink:Article . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence . + rdfs:subClassOf biolink:GeographicLocationAtTime ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeographicLocationAtTime . [] a owl:Restriction ; - rdfs:subClassOf biolink:Haplotype ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Haplotype . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SmallMolecule ; + rdfs:subClassOf biolink:ClinicalMeasurement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SmallMolecule . + owl:someValuesFrom biolink:ClinicalMeasurement . [] a owl:Restriction ; - rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; + rdfs:subClassOf biolink:Snv ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . + owl:someValuesFrom biolink:Snv . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:RelationshipQuantifier . + rdfs:subClassOf biolink:MicroRNA ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MicroRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:EvidenceType ; + rdfs:subClassOf biolink:ProteinFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EvidenceType . + owl:someValuesFrom biolink:ProteinFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + rdfs:subClassOf biolink:CellLine ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + owl:someValuesFrom biolink:CellLine . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genome ; + rdfs:subClassOf biolink:GeneToGoTermAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genome . + owl:someValuesFrom biolink:GeneToGoTermAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugLabel ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugLabel . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], @@ -12917,18 +12994,117 @@ biolink:subject a owl:ObjectProperty ; owl:minCardinality 0 ; owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ] ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Phenomenon ; + rdfs:subClassOf biolink:ChemicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Phenomenon . + owl:someValuesFrom biolink:ChemicalEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BookChapter ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BookChapter . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathognomonicityQuantifier . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ThingWithTaxon . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:JournalArticle ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:JournalArticle . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DrugExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DrugExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:WebPage ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:WebPage . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:IndividualOrganism ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:IndividualOrganism . [] a owl:Restriction ; rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; @@ -12936,77 +13112,78 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:TranscriptionFactorBindingSite . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . + owl:someValuesFrom biolink:VariantToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ExonToTranscriptRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ExonToTranscriptRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:AccessibleDnaRegion ; + rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AccessibleDnaRegion . + owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genotype ; + rdfs:subClassOf biolink:Virus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genotype . + owl:someValuesFrom biolink:Virus . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; + rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToParticipantAssociation . + owl:someValuesFrom biolink:PathologicalAnatomicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivity ; + rdfs:subClassOf biolink:AccessibleDnaRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivity . + owl:someValuesFrom biolink:AccessibleDnaRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; + rdfs:subClassOf biolink:Fungus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . + owl:someValuesFrom biolink:Fungus . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation . + rdfs:subClassOf biolink:Mammal ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Mammal . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + owl:someValuesFrom biolink:Outcome . [] a owl:Restriction ; - rdfs:subClassOf biolink:Procedure ; + rdfs:subClassOf biolink:StudyResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Procedure . + owl:someValuesFrom biolink:StudyResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; + rdfs:subClassOf biolink:NucleosomeModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . + owl:someValuesFrom biolink:NucleosomeModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularComplex ; + rdfs:subClassOf biolink:SocioeconomicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularComplex . + owl:someValuesFrom biolink:SocioeconomicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:CodingSequence ; + rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CodingSequence . + owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; + rdfs:subClassOf biolink:ClinicalFinding ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . + owl:someValuesFrom biolink:ClinicalFinding . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; @@ -13017,203 +13194,127 @@ biolink:subject a owl:ObjectProperty ; owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:expression_site ], + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:expression_site ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ] ; + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ] ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin . +[] a owl:Restriction ; + rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Disease ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Disease . + [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReagentTargetedGene ; + rdfs:subClassOf biolink:Treatment ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReagentTargetedGene . + owl:someValuesFrom biolink:Treatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalMixture ; + rdfs:subClassOf biolink:NucleicAcidEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalMixture . + owl:someValuesFrom biolink:NucleicAcidEntity . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . + rdfs:subClassOf biolink:PhenotypicFeature ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier . + rdfs:subClassOf biolink:Genotype ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Genotype . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SensitivityQuantifier . + rdfs:subClassOf biolink:MacromolecularComplex ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MacromolecularComplex . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; + rdfs:subClassOf biolink:SiRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . + owl:someValuesFrom biolink:SiRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:Polypeptide ; + rdfs:subClassOf biolink:GeneToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Polypeptide . + owl:someValuesFrom biolink:GeneToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularComponent ; + rdfs:subClassOf biolink:MolecularEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularComponent . + owl:someValuesFrom biolink:MolecularEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:TaxonToTaxonAssociation ; + rdfs:subClassOf biolink:Behavior ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TaxonToTaxonAssociation . + owl:someValuesFrom biolink:Behavior . [] a owl:Restriction ; rdfs:subClassOf biolink:OrganismAttribute ; @@ -13221,281 +13322,219 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:OrganismAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToPathwayAssociation . + owl:someValuesFrom biolink:VariantToGeneAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . + rdfs:subClassOf biolink:PathologicalProcess ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PathologicalProcess . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], + owl:allValuesFrom biolink:CellLine ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:id ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalMeasurement ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalMeasurement . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Agent ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Agent . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationToPopulationAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationToPopulationAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalSex ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalSex . - -[] a owl:Restriction ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPathwayAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPathwayAssociation . + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Transcript ; + rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Transcript . + owl:someValuesFrom biolink:NucleicAcidSequenceMotif . [] a owl:Restriction ; - rdfs:subClassOf biolink:Article ; + rdfs:subClassOf biolink:DrugLabel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Article . + owl:someValuesFrom biolink:DrugLabel . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Exon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Exon . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetDistribution ; + rdfs:subClassOf biolink:OrganismTaxon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetDistribution . + owl:someValuesFrom biolink:OrganismTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:PreprintPublication ; + rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PreprintPublication . + owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConfidenceLevel ; + rdfs:subClassOf biolink:Genome ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConfidenceLevel . + owl:someValuesFrom biolink:Genome . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSample ; + rdfs:subClassOf biolink:RNAProductIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSample . + owl:someValuesFrom biolink:RNAProductIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetSummary ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetSummary . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . [] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Outcome . + owl:someValuesFrom biolink:OntologyClass . [] a owl:Restriction ; - rdfs:subClassOf biolink:Food ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Food . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneticInheritance ; + rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneticInheritance . + owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + rdfs:subClassOf biolink:AnatomicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + owl:someValuesFrom biolink:AnatomicalEntity . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . + owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathognomonicityQuantifier . + owl:someValuesFrom biolink:PhysicalEssence . [] a owl:Restriction ; - rdfs:subClassOf biolink:Study ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Study . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ActivityAndBehavior . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Case ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChiSquaredAnalysisResult . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CellularOrganism ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularOrganism . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BioticExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BioticExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFeature ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFeature . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThing ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThing . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcess ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcess . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Onset ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Onset . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:StudyVariable ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyVariable . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:AdministrativeEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AdministrativeEntity . - -[] a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Mammal ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Mammal . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; rdfs:subClassOf biolink:Gene ; @@ -13503,368 +13542,356 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Gene . [] a owl:Restriction ; - rdfs:subClassOf biolink:PlanetaryEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PlanetaryEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:IndividualOrganism ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IndividualOrganism . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalCourse ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalCourse . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:FunctionalAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FunctionalAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPopulationAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPopulationAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexMolecularMixture ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexMolecularMixture . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:RelationshipQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:MicroRNA ; + rdfs:subClassOf biolink:Polypeptide ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MicroRNA . + owl:someValuesFrom biolink:Polypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcessExposure ; + rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcessExposure . + owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; + rdfs:subClassOf biolink:GenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . + owl:someValuesFrom biolink:GenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NoncodingRNAProduct . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:GeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:Event ; + rdfs:subClassOf biolink:BioticExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Event . + owl:someValuesFrom biolink:BioticExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalModifier ; + rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalModifier . + owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SpecificityQuantifier . + rdfs:subClassOf biolink:GenotypeToVariantAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GenotypeToVariantAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysiologicalProcess ; + rdfs:subClassOf biolink:Pathway ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysiologicalProcess . + owl:someValuesFrom biolink:Pathway . [] a owl:Restriction ; - rdfs:subClassOf biolink:Protein ; + rdfs:subClassOf biolink:ChemicalRole ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Protein . + owl:someValuesFrom biolink:ChemicalRole . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; + rdfs:subClassOf biolink:Onset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneAssociation . + owl:someValuesFrom biolink:Onset . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalModifier ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalModifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Event ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Event . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:EnvironmentalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:EnvironmentalExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:LifeStage ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:LifeStage . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RNAProduct ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RNAProduct . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Agent ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Agent . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicSex ; + rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicSex . + owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:SequenceFeatureRelationship . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneFamily ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneFamily . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Haplotype ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Haplotype . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:synonym ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:synonym ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . + owl:someValuesFrom biolink:GeneProductMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:Activity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:Activity . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_percentage ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_percentage ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SiRNA ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SiRNA . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntity . + owl:someValuesFrom biolink:FrequencyQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:CommonDataElement ; + rdfs:subClassOf biolink:PhysicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CommonDataElement . + owl:someValuesFrom biolink:PhysicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PosttranslationalModification ; + rdfs:subClassOf biolink:Drug ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PosttranslationalModification . + owl:someValuesFrom biolink:Drug . [] a owl:Restriction ; - rdfs:subClassOf biolink:Exon ; + rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Exon . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene_or_gene_product ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin . + owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + rdfs:subClassOf biolink:GeographicLocation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + owl:someValuesFrom biolink:GeographicLocation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent . + rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PairwiseMolecularInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneAssociation ; + rdfs:subClassOf biolink:Human ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneAssociation . + owl:someValuesFrom biolink:Human . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; + rdfs:subClassOf biolink:Serial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . + owl:someValuesFrom biolink:Serial . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLine ; + rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLine . + owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicExposure ; + rdfs:subClassOf biolink:PhenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicExposure . + owl:someValuesFrom biolink:PhenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:Disease ; + rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Disease . + owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:JournalArticle ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:JournalArticle . + owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ], + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:synonym ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductMixin . + owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:StudyVariable ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:StudyVariable . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DatasetVersion ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DatasetVersion . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PathologicalProcessExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PathologicalProcessExposure . [] a owl:Restriction ; rdfs:subClassOf biolink:GenotypeToGeneAssociation ; @@ -13872,153 +13899,151 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:GenotypeToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Zygosity ; + rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Zygosity . + owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + rdfs:subClassOf biolink:BiologicalSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToDiseaseAssociation . + owl:someValuesFrom biolink:BiologicalSex . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + owl:someValuesFrom biolink:SensitivityQuantifier . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntity ; + rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntity . + owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:LogOddsAnalysisResult ; + rdfs:subClassOf biolink:CommonDataElement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LogOddsAnalysisResult . + owl:someValuesFrom biolink:CommonDataElement . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:SequenceVariant ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:VariantToEntityAssociationMixin . +[] a owl:Restriction ; + rdfs:subClassOf biolink:Hospitalization ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Hospitalization . + [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene_or_gene_product ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneGroupingMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MaterialSample ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntity ; + rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntity . + owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:GeneToGeneAssociation ; @@ -14026,129 +14051,163 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:GeneToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; + rdfs:subClassOf biolink:BehavioralFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . + owl:someValuesFrom biolink:BehavioralFeature . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin . + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Association ; + rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Association . + owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + rdfs:subClassOf biolink:Book ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + owl:someValuesFrom biolink:Book . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidEntity ; + rdfs:subClassOf biolink:OrganismToOrganismAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidEntity . + owl:someValuesFrom biolink:OrganismToOrganismAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; + rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalAssociation . + owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:ContributorAssociation ; + rdfs:subClassOf biolink:DiagnosticAid ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ContributorAssociation . + owl:someValuesFrom biolink:DiagnosticAid . [] a owl:Restriction ; - rdfs:subClassOf biolink:Vertebrate ; + rdfs:subClassOf biolink:BiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Vertebrate . + owl:someValuesFrom biolink:BiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalExposure ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalExposure . + owl:someValuesFrom biolink:BiologicalProcessOrActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularMixture ; + rdfs:subClassOf biolink:TranscriptToGeneRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularMixture . + owl:someValuesFrom biolink:TranscriptToGeneRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:DatasetDistribution ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:DatasetDistribution . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:SocioeconomicAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:SocioeconomicAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypicSex ; + rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypicSex . + owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Pathway ; + rdfs:subClassOf biolink:EnvironmentalFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Pathway . + owl:someValuesFrom biolink:EnvironmentalFeature . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . + owl:someValuesFrom biolink:SubjectOfInvestigation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Case ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Case . + owl:someValuesFrom biolink:ChemicalToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + rdfs:subClassOf biolink:Procedure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + owl:someValuesFrom biolink:Procedure . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyPopulation ; + rdfs:subClassOf biolink:ComplexChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyPopulation . + owl:someValuesFrom biolink:ComplexChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Bacterium ; + rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Bacterium . + owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:CellularOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:CellularOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToVariantAssociation ; + rdfs:subClassOf biolink:InformationContentEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToVariantAssociation . + owl:someValuesFrom biolink:InformationContentEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GrossAnatomicalStructure ; + rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GrossAnatomicalStructure . + owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToGeneProductRelationship . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:LogOddsAnalysisResult ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:LogOddsAnalysisResult . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RetrievalSource ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RetrievalSource . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalMixture ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalMixture . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -14157,77 +14216,32 @@ biolink:subject a owl:ObjectProperty ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Drug ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseMolecularInteraction ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseMolecularInteraction . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinDomain ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinDomain . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Cell ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cell . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ExonToTranscriptRelationship ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExonToTranscriptRelationship . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Snv ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Snv . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . + owl:someValuesFrom biolink:DrugToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Invertebrate ; + rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Invertebrate . + owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalRole ; + rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalRole . + owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:Cohort ; @@ -14235,314 +14249,300 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Cohort . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProduct ; + rdfs:subClassOf biolink:ProteinIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProduct . + owl:someValuesFrom biolink:ProteinIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamily ; + rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamily . + owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Publication ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Publication . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:SeverityValue ; + rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SeverityValue . + owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:GeographicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:GeographicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinIsoform ; + rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinIsoform . + owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGoTermAssociation ; + rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGoTermAssociation . + owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:Food ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . + owl:someValuesFrom biolink:Food . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; + rdfs:subClassOf biolink:PreprintPublication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + owl:someValuesFrom biolink:PreprintPublication . [] a owl:Restriction ; - rdfs:subClassOf biolink:RegulatoryRegion ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RegulatoryRegion . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + owl:someValuesFrom biolink:PathologicalAnatomicalStructure . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior . + rdfs:subClassOf biolink:Transcript ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Transcript . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralExposure ; + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralExposure . + owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConceptCountAnalysisResult ; + rdfs:subClassOf biolink:CodingSequence ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConceptCountAnalysisResult . + owl:someValuesFrom biolink:CodingSequence . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; + rdfs:subClassOf biolink:ComplexMolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . + owl:someValuesFrom biolink:ComplexMolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysicalEntity ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysicalEntity . + owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; + rdfs:subClassOf biolink:SequenceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . + owl:someValuesFrom biolink:SequenceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Activity ; + rdfs:subClassOf biolink:PosttranslationalModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Activity . + owl:someValuesFrom biolink:PosttranslationalModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:Zygosity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:Zygosity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Attribute ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Attribute . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathologicalEntityMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetVersion ; + rdfs:subClassOf biolink:ReagentTargetedGene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetVersion . + owl:someValuesFrom biolink:ReagentTargetedGene . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:BiologicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:BiologicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; + rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . + owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; + rdfs:subClassOf biolink:CellularComponent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + owl:someValuesFrom biolink:CellularComponent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Device ; + rdfs:subClassOf biolink:EntityToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Device . + owl:someValuesFrom biolink:EntityToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralFeature ; + rdfs:subClassOf biolink:EvidenceType ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralFeature . + owl:someValuesFrom biolink:EvidenceType . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicAttribute ; + rdfs:subClassOf biolink:Attribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicAttribute . + owl:someValuesFrom biolink:Attribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcess ; + rdfs:subClassOf biolink:Publication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcess . + owl:someValuesFrom biolink:Publication . [] a owl:Restriction ; - rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . + owl:someValuesFrom biolink:ChemicalToChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Outcome ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . + rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DrugToGeneInteractionExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicBackgroundExposure ; + rdfs:subClassOf biolink:StudyPopulation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicBackgroundExposure . + owl:someValuesFrom biolink:StudyPopulation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiagnosticAid ; + rdfs:subClassOf biolink:DatasetSummary ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiagnosticAid . + owl:someValuesFrom biolink:DatasetSummary . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidSequenceMotif . + owl:someValuesFrom biolink:NoncodingRNAProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:Virus ; + rdfs:subClassOf biolink:ClinicalCourse ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Virus . + owl:someValuesFrom biolink:ClinicalCourse . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; + rdfs:subClassOf biolink:AdministrativeEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . + owl:someValuesFrom biolink:AdministrativeEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . + owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BookChapter ; + rdfs:subClassOf biolink:ClinicalTrial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BookChapter . + owl:someValuesFrom biolink:ClinicalTrial . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexChemicalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexChemicalExposure . + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntity ; + rdfs:subClassOf biolink:ContributorAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntity . + owl:someValuesFrom biolink:ContributorAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + rdfs:subClassOf biolink:Patent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . + owl:someValuesFrom biolink:Patent . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalIntervention ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalIntervention . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductIsoformMixin . diff --git a/project/prefixmap/biolink-model-prefix-map.json b/project/prefixmap/biolink-model-prefix-map.json index ffc9dfb5e..5319bdeff 100644 --- a/project/prefixmap/biolink-model-prefix-map.json +++ b/project/prefixmap/biolink-model-prefix-map.json @@ -259,4 +259,4 @@ "skos": "http://www.w3.org/2004/02/skos/core#", "wgs": "http://www.w3.org/2003/01/geo/wgs84_pos", "xsd": "http://www.w3.org/2001/XMLSchema#" -} +} \ No newline at end of file diff --git a/project/protobuf/biolink_model.proto b/project/protobuf/biolink_model.proto index e8052a941..8dd5b8b2d 100644 --- a/project/protobuf/biolink_model.proto +++ b/project/protobuf/biolink_model.proto @@ -1,3 +1,7 @@ + syntax="proto3"; + package +// metamodel_version: 1.7.0 +// version: 4.2.4 // A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose message AccessibleDnaRegion { diff --git a/project/shacl/biolink_model.shacl.ttl b/project/shacl/biolink_model.shacl.ttl index 8a16f0947..59f40a22c 100644 --- a/project/shacl/biolink_model.shacl.ttl +++ b/project/shacl/biolink_model.shacl.ttl @@ -7,332 +7,313 @@ @prefix xsd: . biolink:AccessibleDnaRegion a sh:NodeShape ; + rdfs:subClassOf biolink:RegulatoryRegion ; sh:closed true ; sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:AccessibleDnaRegion . - -biolink:Activity a sh:NodeShape ; - sh:closed true ; - sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Activity . + sh:path biolink:category ] ; + sh:targetClass biolink:AccessibleDnaRegion . biolink:ActivityAndBehavior a sh:NodeShape ; + rdfs:subClassOf biolink:Occurrent ; sh:closed false ; sh:description "Activity or behavior of any independent integral living, organization or mechanical actor in the world" ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:ActivityAndBehavior . -biolink:AdministrativeEntity a sh:NodeShape ; - sh:closed false ; +biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:AdministrativeEntity . - -biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "the structure at a later time" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -345,1608 +326,3848 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the part" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the whole" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the part" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + +biolink:Bacterium a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismalEntity ; + sh:closed true ; + sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the whole" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . - -biolink:Annotation a sh:NodeShape ; - sh:closed false ; - sh:description "Biolink Model root class for entity annotations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:Annotation . - -biolink:Article a sh:NodeShape ; - sh:closed true ; - sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 7 ; - sh:path biolink:keywords ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 5 ; - sh:path biolink:pages ], + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 21 ; - sh:path rdf:type ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path dct:description ], + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:id ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:Bacterium . + +biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:license ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 25 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; sh:path biolink:deprecated ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:iri ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 10 ; - sh:path dct:type ], + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:summary ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:issue ] ; - sh:targetClass biolink:Article . - -biolink:Association a sh:NodeShape ; - sh:closed true ; - sh:description "A typed association between two entities, supported by evidence" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:has_evidence ], + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; sh:order 28 ; - sh:path biolink:p_value ], + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:id ], - [ sh:description "a point in time" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:BehavioralFeature ; + sh:description "behavioral feature that is the object of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 19 ; sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ] ; - sh:targetClass biolink:Association . + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . -biolink:Bacterium a sh:NodeShape ; +biolink:BehavioralExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; + sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:Bacterium . - -biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ] ; + sh:targetClass biolink:BehavioralExposure . + +biolink:BehavioralOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An outcome resulting from an exposure event which is the manifestation of human behavior." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:BehavioralOutcome . + +biolink:BioticExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; + sh:closed true ; + sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:BioticExposure . + +biolink:Book a sh:NodeShape ; + rdfs:subClassOf biolink:Publication ; + sh:closed true ; + sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:BehavioralFeature ; - sh:description "behavioral feature that is the object of the association" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; + sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Books should have industry-standard identifier such as from ISBN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'book'." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path biolink:provided_by ] ; + sh:targetClass biolink:Book . + +biolink:BookChapter a sh:NodeShape ; + rdfs:subClassOf biolink:Publication ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:format ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:type ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:volume ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:negated ], + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 37 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; sh:path dct:description ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ] ; - sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . - -biolink:BehavioralExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:datatype xsd:string ; + sh:description "chapter of a book" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:chapter ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:path biolink:license ] ; + sh:targetClass biolink:BookChapter . + +biolink:CaseToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An abstract association for use where the case is the subject" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:BehavioralExposure . + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:CaseToEntityAssociationMixin . -biolink:BehavioralOutcome a sh:NodeShape ; +biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of human behavior." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:BehavioralOutcome . - -biolink:BiologicalEntity a sh:NodeShape ; - sh:closed false ; + sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 38 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Case ; + sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:BiologicalEntity . - -biolink:BiologicalProcessOrActivity a sh:NodeShape ; - sh:closed true ; - sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 13 ; - sh:path rdfs:label ], + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_input ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path dct:description ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:enabled_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_output ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:BiologicalProcessOrActivity . - -biolink:BioticExposure a sh:NodeShape ; - sh:closed true ; - sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . + +biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ] ; + sh:targetClass biolink:CausalGeneToDiseaseAssociation . + +biolink:Cell a sh:NodeShape ; + rdfs:subClassOf biolink:AnatomicalEntity ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:Cell . + +biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + +biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An relationship between a cell line and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:CellLine ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:CellLineToEntityAssociationMixin . + +biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:original_object ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:original_subject ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 45 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:subject_closure ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:object_category ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 52 ; + sh:path biolink:has_attribute ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 17 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:object_category_closure ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:p_value ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path rdf:subject ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:species_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:publications ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . + +biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . + +biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "A regulatory relationship between two genes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "the direction is always from regulator to regulated" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + +biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; + sh:closed false ; + sh:description "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:ChemicalEntityOrProteinOrPolypeptide . + +biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path dct:description ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 10 ; + sh:path rdf:object ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:subject_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 45 ; sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path rdf:type ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:id ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:ChemicalGeneInteractionAssociation . + +biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:ChemicalOrDrugOrTreatment . + +biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; + sh:closed true ; + sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:BioticExposure . + sh:path biolink:qualifier ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . -biolink:Book a sh:NodeShape ; +biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; sh:closed true ; - sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; + sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the downstream chemical entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Books should have industry-standard identifier such as from ISBN." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:creation_date ], + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'book'." ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:license ], + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the upstream chemical entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Book . + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . -biolink:BookChapter a sh:NodeShape ; +biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; + sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "chapter of a book" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:chapter ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:description "mesh terms tagging a publication" ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 22 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; - sh:path biolink:category ], + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 16 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 12 ; - sh:path biolink:format ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:volume ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:order 20 ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 9 ; - sh:path dct:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:BookChapter . + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; + sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . -biolink:CaseToEntityAssociationMixin a sh:NodeShape ; +biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalEntityToEntityAssociationMixin ; sh:closed false ; - sh:description "An abstract association for use where the case is the subject" ; + sh:description "An interaction between a chemical entity and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -1954,8976 +4175,10194 @@ biolink:CaseToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:CaseToEntityAssociationMixin . + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:ChemicalToEntityAssociationMixin . -biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:ChemicalToPathwayAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; + sh:description "An interaction between a chemical entity and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; sh:order 37 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:path biolink:agent_type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Case ; - sh:description "the case (e.g. patient) that has the property" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 17 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . - -biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:agent_type ], + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 17 ; sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:ChemicalToPathwayAssociation . + +biolink:ChiSquaredAnalysisResult a sh:NodeShape ; + rdfs:subClassOf biolink:StudyResult ; + sh:closed true ; + sh:description "A result of a chi squared analysis." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:path rdf:type ] ; + sh:targetClass biolink:ChiSquaredAnalysisResult . + +biolink:ClinicalFinding a sh:NodeShape ; + rdfs:subClassOf biolink:PhenotypicFeature ; + sh:closed true ; + sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 35 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:ClinicalAttribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ClinicalFinding . + +biolink:ClinicalMeasurement a sh:NodeShape ; + rdfs:subClassOf biolink:ClinicalAttribute ; + sh:closed true ; + sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 40 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ] ; - sh:targetClass biolink:CausalGeneToDiseaseAssociation . - -biolink:Cell a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:ClinicalMeasurement . + +biolink:ClinicalModifier a sh:NodeShape ; + rdfs:subClassOf biolink:ClinicalAttribute ; + sh:closed true ; + sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ] ; + sh:targetClass biolink:ClinicalModifier . + +biolink:ClinicalTrial a sh:NodeShape ; + rdfs:subClassOf biolink:ClinicalEntity ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:Cell . - -biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:path rdfs:label ] ; + sh:targetClass biolink:ClinicalTrial . + +biolink:CodingSequence a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:CodingSequence . + +biolink:Cohort a sh:NodeShape ; + rdfs:subClassOf biolink:StudyPopulation ; + sh:closed true ; + sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:timepoint ], + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 35 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Cohort . + +biolink:CommonDataElement a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; + sh:closed true ; + sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:has_evidence ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "The relationship to the disease" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; - sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:CommonDataElement . -biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:ComplexChemicalExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; + sh:targetClass biolink:ComplexChemicalExposure . + +biolink:ComplexMolecularMixture a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalMixture ; + sh:closed true ; + sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 36 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:available_from ] ; + sh:targetClass biolink:ComplexMolecularMixture . + +biolink:ConceptCountAnalysisResult a sh:NodeShape ; + rdfs:subClassOf biolink:StudyResult ; + sh:closed true ; + sh:description "A result of a concept count analysis." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:license ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . - -biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An relationship between a cell line and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:CellLine ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:CellLineToEntityAssociationMixin . + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ConceptCountAnalysisResult . -biolink:CellularOrganism a sh:NodeShape ; +biolink:ConfidenceLevel a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; sh:closed true ; - sh:description "" ; + sh:description "Level of confidence in a statement" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:CellularOrganism . + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ConfidenceLevel . -biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; +biolink:ContributorAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; + sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 52 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 24 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:Agent ; + sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 17 ; - sh:path rdf:object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 48 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_evidence ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 11 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 50 ; - sh:path rdfs:label ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 49 ; - sh:path rdf:type ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 40 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:InformationContentEntity ; + sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 0 ; sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 51 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 53 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:negated ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:subject_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:AnatomicalEntity ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 25 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 35 ; - sh:path biolink:object_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 43 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 45 ; + sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 46 ; - sh:path biolink:id ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 34 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 41 ; - sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:species_context_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; + sh:targetClass biolink:ContributorAssociation . -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; +biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; + sh:property [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 29 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:id ], + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to correlate with the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ] ; + sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . -biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; +biolink:DatasetSummary a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; sh:closed true ; - sh:description "A regulatory relationship between two genes" ; + sh:description "an item that holds summary level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path schema1:logo ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:source_web_page ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 16 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:rights ] ; + sh:targetClass biolink:DatasetSummary . + +biolink:DatasetVersion a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; + sh:closed true ; + sh:description "an item that holds version level information about a dataset." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Dataset ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 0 ; + sh:path biolink:has_dataset ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:original_subject ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:format ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:ingest_date ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:class biolink:DatasetDistribution ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path dct:distribution ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:rights ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; sh:path biolink:deprecated ], - [ sh:description "the direction is always from regulator to regulated" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path rdf:object ], + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . - -biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; - sh:closed false ; - sh:description "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalEntityOrProteinOrPolypeptide . + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ] ; + sh:targetClass biolink:DatasetVersion . -biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An interaction between a chemical entity and another entity" ; +biolink:DiagnosticAid a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed true ; + sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity that is an interactor" ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:DiagnosticAid . -biolink:ChemicalExposure a sh:NodeShape ; +biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "A chemical exposure is an intake of a particular chemical entity." ; + sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; + sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . + +biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureOutcome . + +biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:path rdf:object ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:ChemicalExposure . + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . -biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; +biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; + sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 34 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; sh:path biolink:object_closure ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 42 ; - sh:path rdf:type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_supporting_studies ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 37 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 27 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:subject_context_qualifier ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_part_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 41 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 39 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 18 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 44 ; - sh:path dct:description ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:GeneticInheritance ; + sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 10 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ChemicalGeneInteractionAssociation . - -biolink:ChemicalMixture a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 11 ; - sh:path biolink:full_name ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:object_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:id ] ; - sh:targetClass biolink:ChemicalMixture . - -biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalOrDrugOrTreatment . + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . -biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; + sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:FDA_adverse_event_level ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 6 ; sh:path biolink:publications ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:object_closure ], + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:negated ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 22 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + +biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:DiseaseToEntityAssociationMixin . -biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; + sh:description "An association between an exposure event and a disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:subject_closure ], + sh:path biolink:object_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:qualifiers ], + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:agent_type ], + sh:path biolink:timepoint ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 31 ; + sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:subject ], + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path rdf:type ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalToChemicalAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:DiseaseToExposureEventAssociation . + +biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_count ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 48 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 43 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 3 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 24 ; sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:ChemicalToChemicalAssociation . - -biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:onset_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:timepoint ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 8 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 28 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 27 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 18 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:deprecated ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 13 ; sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ] ; + sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . + +biolink:DrugLabel a sh:NodeShape ; + rdfs:subClassOf biolink:Publication ; + sh:closed true ; + sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:catalyst_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path rdf:object ], + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 33 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ] ; + sh:targetClass biolink:DrugLabel . -biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; +biolink:DrugToEntityAssociationMixin a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalEntityToEntityAssociationMixin ; + sh:closed false ; + sh:description "An interaction between a drug and another entity" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:DrugToEntityAssociationMixin . + +biolink:DrugToGeneAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An interaction between a drug and a gene or gene product." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "the disease or phenotype that is affected by the chemical" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Drug ; + sh:description "the drug that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . - -biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An interaction between a chemical entity and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:ChemicalToEntityAssociationMixin . - -biolink:ChemicalToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a chemical entity and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:DrugToGeneAssociation . + +biolink:DrugToGeneInteractionExposure a sh:NodeShape ; + rdfs:subClassOf biolink:DrugExposure ; + sh:closed true ; + sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 4 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; + sh:targetClass biolink:DrugToGeneInteractionExposure . + +biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 3 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that is affected by the chemical" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:ChemicalToPathwayAssociation . - -biolink:ChiSquaredAnalysisResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of a chi squared analysis." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path rdfs:label ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 40 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:ChiSquaredAnalysisResult . - -biolink:ClinicalCourse a sh:NodeShape ; - sh:closed true ; - sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:description "connects an association to an instance of supporting evidence" ; + sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; - sh:targetClass biolink:ClinicalCourse . + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ] ; + sh:targetClass biolink:DruggableGeneToDiseaseAssociation . -biolink:ClinicalEntity a sh:NodeShape ; +biolink:EntityToDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 39 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ] ; - sh:targetClass biolink:ClinicalEntity . - -biolink:ClinicalFinding a sh:NodeShape ; - sh:closed true ; - sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:path biolink:max_research_phase ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:ClinicalAttribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:ClinicalFinding . - -biolink:ClinicalIntervention a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ClinicalIntervention . + sh:path rdf:object ] ; + sh:targetClass biolink:EntityToDiseaseAssociation . -biolink:ClinicalMeasurement a sh:NodeShape ; - sh:closed true ; - sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; +biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; + rdfs:subClassOf biolink:EntityToFeatureOrDiseaseQualifiersMixin ; + sh:closed false ; + sh:description "mixin class for any association whose object (target node) is a disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ClinicalMeasurement . + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ] ; + sh:targetClass biolink:EntityToDiseaseAssociationMixin . -biolink:ClinicalModifier a sh:NodeShape ; - sh:closed true ; - sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; +biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; + sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + +biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An association between some entity and an exposure event." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ClinicalModifier . + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:EntityToExposureEventAssociationMixin . -biolink:ClinicalTrial a sh:NodeShape ; - sh:closed true ; +biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An association between some entity and an outcome" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ] ; - sh:targetClass biolink:ClinicalTrial . + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:EntityToOutcomeAssociationMixin . -biolink:CodingSequence a sh:NodeShape ; +biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:CodingSequence . - -biolink:Cohort a sh:NodeShape ; - sh:closed true ; - sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 1 ; + sh:path biolink:max_research_phase ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:Cohort . - -biolink:CommonDataElement a sh:NodeShape ; - sh:closed true ; - sh:description "A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. (https://cde.nlm.nih.gov/home)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 39 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . + +biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; + rdfs:subClassOf biolink:EntityToFeatureOrDiseaseQualifiersMixin ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:CommonDataElement . + sh:order 9 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:has_percentage ] ; + sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . -biolink:ComplexChemicalExposure a sh:NodeShape ; +biolink:EnvironmentalFeature a sh:NodeShape ; + rdfs:subClassOf biolink:PlanetaryEntity ; sh:closed true ; - sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 11 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ] ; - sh:targetClass biolink:ComplexChemicalExposure . + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:EnvironmentalFeature . -biolink:ComplexMolecularMixture a sh:NodeShape ; +biolink:EnvironmentalFoodContaminant a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalEntity ; sh:closed true ; - sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:is_toxic ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:synonym ], + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 18 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ] ; - sh:targetClass biolink:ComplexMolecularMixture . + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ] ; + sh:targetClass biolink:EnvironmentalFoodContaminant . -biolink:ConceptCountAnalysisResult a sh:NodeShape ; +biolink:EnvironmentalProcess a sh:NodeShape ; + rdfs:subClassOf biolink:PlanetaryEntity ; sh:closed true ; - sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:xref ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:ConceptCountAnalysisResult . + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ] ; + sh:targetClass biolink:EnvironmentalProcess . -biolink:ConfidenceLevel a sh:NodeShape ; +biolink:EpidemiologicalOutcome a sh:NodeShape ; sh:closed true ; - sh:description "Level of confidence in a statement" ; + sh:description "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:EpidemiologicalOutcome . + +biolink:EpigenomicEntity a sh:NodeShape ; + sh:closed false ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:EpigenomicEntity . + +biolink:Event a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed true ; + sh:description "Something that happens at a given place and time." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:provided_by ], + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ConfidenceLevel . + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:Event . -biolink:ContributorAssociation a sh:NodeShape ; +biolink:ExonToTranscriptRelationship a sh:NodeShape ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; sh:closed true ; - sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; + sh:description "A transcript is formed from multiple exons" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:Transcript ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Exon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:ExonToTranscriptRelationship . + +biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An association between an exposure event and an outcome." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:time ; + sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 0 ; + sh:path biolink:population_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; sh:path rdf:type ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 28 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:InformationContentEntity ; - sh:description "information content entity which an agent has helped realise" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ] ; - sh:targetClass biolink:ContributorAssociation . - -biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], + sh:order 8 ; + sh:path biolink:publications ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 32 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; sh:order 7 ; - sh:path biolink:qualifier ], + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 40 ; + sh:order 39 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:double ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ExposureEventToOutcomeAssociation . + +biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 46 ; + sh:order 45 ; sh:path biolink:subject_direction_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:publications ], + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; + sh:order 13 ; sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; sh:path biolink:p_value ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to correlate with the disease." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 49 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], + sh:path biolink:object_category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ] ; - sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . - -biolink:DatasetSummary a sh:NodeShape ; - sh:closed true ; - sh:description "an item that holds summary level information about a dataset." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:source_web_page ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:format ], + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path schema1:logo ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:rights ] ; - sh:targetClass biolink:DatasetSummary . + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ] ; + sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . -biolink:DatasetVersion a sh:NodeShape ; +biolink:Food a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalMixture ; sh:closed true ; - sh:description "an item that holds version level information about a dataset." ; + sh:description "A substance consumed by a living organism as a source of nutrition" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 18 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:ingest_date ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:order 14 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:creation_date ], + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path biolink:has_attribute ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:rights ], - [ sh:class biolink:Dataset ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_dataset ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:DatasetDistribution ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ] ; - sh:targetClass biolink:DatasetVersion . - -biolink:DiagnosticAid a sh:NodeShape ; - sh:closed true ; - sh:description "A device or substance used to help diagnose disease or injury" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:DiagnosticAid . + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ] ; + sh:targetClass biolink:Food . -biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; +biolink:FoodAdditive a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalEntity ; sh:closed true ; - sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path rdfs:label ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:timepoint ], + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . - -biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureOutcome . + sh:path biolink:xref ] ; + sh:targetClass biolink:FoodAdditive . -biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; +biolink:FrequencyQuantifier a sh:NodeShape ; + rdfs:subClassOf biolink:RelationshipQuantifier ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:has_count ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_total ] ; + sh:targetClass biolink:FrequencyQuantifier . -biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape ; +biolink:Fungus a sh:NodeShape ; + rdfs:subClassOf biolink:CellularOrganism ; sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; + sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:qualifiers ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ] ; + sh:targetClass biolink:Fungus . + +biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 21 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:GeneticInheritance ; - sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 18 ; sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 7 ; + sh:path biolink:object_part_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 38 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:path biolink:timepoint ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . - -biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 46 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:IRI ; sh:order 34 ; - sh:path rdf:type ], + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 52 ; + sh:path dct:description ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 23 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 9 ; + sh:path biolink:object_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 53 ; sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_namespace ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 54 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 35 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 15 ; + sh:path biolink:species_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . - -biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 33 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 28 ; + sh:path biolink:agent_type ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:DiseaseToEntityAssociationMixin . - -biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an exposure event and a disease." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path biolink:object_derivative_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path rdf:type ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 16 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; + sh:order 43 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:p_value ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ] ; + sh:targetClass biolink:GeneAffectsChemicalAssociation . + +biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 8 ; sh:path biolink:qualifiers ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:object_category ], + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 25 ; sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 14 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 40 ; sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 32 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; sh:path biolink:iri ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:DiseaseToExposureEventAssociation . + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ] ; + sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . -biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; +biolink:GeneExpressionMixin a sh:NodeShape ; + sh:closed false ; + sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ] ; + sh:targetClass biolink:GeneExpressionMixin . + +biolink:GeneGroupingMixin a sh:NodeShape ; + sh:closed false ; + sh:description "any grouping of multiple genes or gene products" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ] ; + sh:targetClass biolink:GeneGroupingMixin . + +biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; sh:path biolink:has_count ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:double ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 22 ; sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:negated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_total ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:onset_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 3 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 22 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 40 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 32 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_total ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category_closure ], + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 48 ; + sh:order 5 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 43 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sex_qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 37 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; sh:path biolink:id ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 39 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . - -biolink:DrugExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A drug exposure is an intake of a particular drug." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 0 ; + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:timepoint ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . + +biolink:GeneProductIsoformMixin a sh:NodeShape ; + rdfs:subClassOf biolink:GeneProductMixin ; + sh:closed false ; + sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:DrugExposure . + sh:path biolink:xref ] ; + sh:targetClass biolink:GeneProductIsoformMixin . -biolink:DrugLabel a sh:NodeShape ; +biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; + sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ] ; - sh:targetClass biolink:DrugLabel . - -biolink:DrugToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An interaction between a drug and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:DrugToEntityAssociationMixin . - -biolink:DrugToGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a drug and a gene or gene product." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 11 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 13 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; sh:path biolink:deprecated ], + [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path biolink:knowledge_source ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:negated ], + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 28 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path rdf:object ] ; + sh:targetClass biolink:GeneRegulatesGeneAssociation . + +biolink:GeneToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Drug ; - sh:description "the drug that is an interactor" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:GeneToEntityAssociationMixin . + +biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:id ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product that is affected by the drug" ; + sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; - sh:path rdf:object ], + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:negated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 7 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "expression relationship" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], + [ sh:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 0 ; + sh:path biolink:stage_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "can be used to indicate magnitude, or also ranking" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:quantifier_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; + sh:order 29 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:DrugToGeneAssociation . - -biolink:DrugToGeneInteractionExposure a sh:NodeShape ; - sh:closed true ; - sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 13 ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; sh:path rdf:type ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 8 ; - sh:path biolink:provided_by ], - [ sh:description "a point in time" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:full_name ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:category ], + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 11 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ] ; - sh:targetClass biolink:DrugToGeneInteractionExposure . - -biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 24 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:GeneToExpressionSiteAssociation . + +biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; + sh:closed true ; + sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 41 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; sh:path biolink:deprecated ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 12 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:qualifiers ], + sh:path biolink:qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 40 ; + sh:order 41 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 27 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:description "connects an association to an instance of supporting evidence" ; - sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], + sh:path biolink:publications ], [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; + sh:order 4 ; sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:datatype xsd:double ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ] ; - sh:targetClass biolink:DruggableGeneToDiseaseAssociation . - -biolink:Entity a sh:NodeShape ; - sh:closed false ; - sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 3 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:negated ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 2 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Entity . - -biolink:EntityToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; + sh:order 15 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 22 ; - sh:path biolink:object_closure ], + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 18 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; + sh:order 11 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ] ; + sh:targetClass biolink:GeneToGeneCoexpressionAssociation . + +biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "membership of the gene in the given gene family." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:path rdf:predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:EntityToDiseaseAssociation . - -biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "mixin class for any association whose object (target node) is a disease" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:EntityToDiseaseAssociationMixin . - -biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . - -biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An association between some entity and an exposure event." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:ExposureEvent ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:GeneFamily ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:EntityToExposureEventAssociationMixin . + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; + sh:targetClass biolink:GeneToGeneFamilyAssociation . -biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; - sh:closed false ; - sh:description "Qualifiers for entity to disease or phenotype associations." ; +biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; + sh:closed true ; + sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ] ; - sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . - -biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An association between some entity and an outcome" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "homology relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:EntityToOutcomeAssociationMixin . - -biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:description "a point in time" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:qualifiers ], + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 29 ; + sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 22 ; - sh:path biolink:object_closure ], + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 25 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:GeneToGeneHomologyAssociation . + +biolink:GeneToGeneProductRelationship a sh:NodeShape ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; + sh:closed true ; + sh:description "A gene is transcribed and potentially translated to a gene product" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 30 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . - -biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:has_percentage ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:qualified_predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:double ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:PhenotypicFeature ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:GeneProductMixin ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:has_total ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ] ; - sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . - -biolink:EnvironmentalExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ] ; - sh:targetClass biolink:EnvironmentalExposure . + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:GeneToGeneProductRelationship . -biolink:EnvironmentalFeature a sh:NodeShape ; +biolink:GeneToGoTermAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:FunctionalAssociation ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:EnvironmentalFeature . - -biolink:EnvironmentalFoodContaminant a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdf:subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; - sh:path biolink:category ], + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:EnvironmentalFoodContaminant . - -biolink:EnvironmentalProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:EnvironmentalProcess . - -biolink:EpidemiologicalOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:EpidemiologicalOutcome . - -biolink:EpigenomicEntity a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; - sh:targetClass biolink:EpigenomicEntity . - -biolink:Event a sh:NodeShape ; - sh:closed true ; - sh:description "Something that happens at a given place and time." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:order 7 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:Event . + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:GeneToGoTermAssociation . -biolink:ExonToTranscriptRelationship a sh:NodeShape ; +biolink:GeneToPathwayAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "A transcript is formed from multiple exons" ; + sh:description "An interaction between a gene or gene product and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Exon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ] ; + sh:targetClass biolink:GeneToPathwayAssociation . + +biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Transcript ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; + sh:order 33 ; sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; - sh:targetClass biolink:ExonToTranscriptRelationship . - -biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between an exposure event and an outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:population_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 25 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 39 ; + sh:order 40 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; sh:order 30 ; - sh:path biolink:p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . + +biolink:Genome a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:description "A genome is the sum of genetic material within a cell or virion." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 33 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 40 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:ExposureEventToOutcomeAssociation . + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ] ; + sh:targetClass biolink:Genome . -biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:GenomicBackgroundExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; + sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:full_name ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 1 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 9 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 8 ; + sh:path biolink:has_quantitative_value ] ; + sh:targetClass biolink:GenomicBackgroundExposure . + +biolink:GenomicEntity a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:GenomicEntity . + +biolink:GenomicSequenceLocalization a sh:NodeShape ; + rdfs:subClassOf biolink:SequenceAssociation ; + sh:closed true ; + sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:order 4 ; + sh:path biolink:phase ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 10 ; sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; sh:path biolink:original_subject ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:start_interbase_coordinate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 11 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; + sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 2 ; + sh:path biolink:genome_build ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . - -biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; - sh:closed false ; - sh:description "Qualifiers for disease or phenotype to entity associations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:NucleicAcidEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; + sh:order 7 ; sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . - -biolink:Food a sh:NodeShape ; - sh:closed true ; - sh:description "A substance consumed by a living organism as a source of nutrition" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 18 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:order 16 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:end_interbase_coordinate ], + [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; + sh:in ( "+" "-" "." "?" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Food . + sh:order 3 ; + sh:path biolink:strand ] ; + sh:targetClass biolink:GenomicSequenceLocalization . -biolink:FoodAdditive a sh:NodeShape ; +biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:order 11 ; - sh:path biolink:category ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:FoodAdditive . - -biolink:FrequencyQualifierMixin a sh:NodeShape ; - sh:closed false ; - sh:description "Qualifier for frequency type associations" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:FrequencyQualifierMixin . - -biolink:FrequencyQuantifier a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:double ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_quotient ] ; - sh:targetClass biolink:FrequencyQuantifier . - -biolink:FunctionalAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "a point in time" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . + +biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:GenotypeToEntityAssociationMixin . + +biolink:GenotypeToGeneAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], [ sh:class biolink:Study ; @@ -10931,6779 +14370,7936 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "the relationship type used to connect genotype to gene" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Gene ; + sh:description "gene implicated in genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:FunctionalAssociation . - -biolink:Fungus a sh:NodeShape ; - sh:closed true ; - sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:order 9 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:Fungus . + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ] ; + sh:targetClass biolink:GenotypeToGeneAssociation . -biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; +biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; + sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 51 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 38 ; + sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; sh:order 30 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 49 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:object_category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 47 ; - sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 54 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 26 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:in ( "metabolite" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 46 ; - sh:path biolink:has_supporting_studies ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 24 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:timepoint ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:AnatomicalEntity ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Genotype ; + sh:description "child genotype" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 19 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 41 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:AnatomicalEntity ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:object_context_qualifier ], + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 43 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 42 ; - sh:path biolink:object_label_closure ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:object_namespace ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 52 ; - sh:path dct:description ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:qualifier ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path rdf:object ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 35 ; - sh:path biolink:subject_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:GenotypeToGenotypePartAssociation . + +biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 7 ; sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 53 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 50 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 16 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:GeneAffectsChemicalAssociation . - -biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:double ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 3 ; sh:path biolink:sex_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:description "The relationship to the disease" ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 18 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:iri ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], + sh:path biolink:has_total ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 8 ; sh:path biolink:has_evidence ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 19 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . - -biolink:GeneExpressionMixin a sh:NodeShape ; - sh:closed false ; - sh:description "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ] ; - sh:targetClass biolink:GeneExpressionMixin . - -biolink:GeneGroupingMixin a sh:NodeShape ; - sh:closed false ; - sh:description "any grouping of multiple genes or gene products" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ] ; - sh:targetClass biolink:GeneGroupingMixin . + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . -biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; +biolink:GenotypeToVariantAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; + sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_total ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 41 ; + sh:order 37 ; sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:description "a point in time" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:GenotypeToVariantAssociation . + +biolink:GenotypicSex a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalSex ; + sh:closed true ; + sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:has_evidence ], + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:publications ], + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:double ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:GenotypicSex . + +biolink:GeographicExposure a sh:NodeShape ; + rdfs:subClassOf biolink:EnvironmentalExposure ; + sh:closed true ; + sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:sex_qualifier ], + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ] ; + sh:targetClass biolink:GeographicExposure . + +biolink:GeographicLocationAtTime a sh:NodeShape ; + rdfs:subClassOf biolink:GeographicLocation ; + sh:closed true ; + sh:description "a location that can be described in lat/long coordinates, for a particular time" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "latitude" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:latitude ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "longitude" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:longitude ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 42 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ] ; - sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . - -biolink:GeneProductIsoformMixin a sh:NodeShape ; - sh:closed false ; - sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:xref ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:GeneProductIsoformMixin . + sh:path biolink:timepoint ] ; + sh:targetClass biolink:GeographicLocationAtTime . -biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; +biolink:GrossAnatomicalStructure a sh:NodeShape ; + rdfs:subClassOf biolink:AnatomicalEntity ; sh:closed true ; - sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 42 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:GrossAnatomicalStructure . + +biolink:Haplotype a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 41 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 35 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ] ; + sh:targetClass biolink:Haplotype . + +biolink:Hospitalization a sh:NodeShape ; + rdfs:subClassOf biolink:ClinicalIntervention ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:Hospitalization . + +biolink:HospitalizationOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:HospitalizationOutcome . + +biolink:Human a sh:NodeShape ; + rdfs:subClassOf biolink:Mammal ; + sh:closed true ; + sh:description "A member of the the species Homo sapiens." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 0 ; - sh:path biolink:object_aspect_qualifier ], + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:publications ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:GeneRegulatesGeneAssociation . + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:Human . -biolink:GeneToDiseaseAssociation a sh:NodeShape ; +biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; + sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; + sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:timepoint ], + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; + sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 27 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . + +biolink:Invertebrate a sh:NodeShape ; + rdfs:subClassOf biolink:CellularOrganism ; + sh:closed true ; + sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:Invertebrate . -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:JournalArticle a sh:NodeShape ; + rdfs:subClassOf biolink:Article ; sh:closed true ; + sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path dct:type ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 4 ; + sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 22 ; sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:pages ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:path biolink:summary ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path dct:description ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], + sh:order 24 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], + [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:issue ] ; + sh:targetClass biolink:JournalArticle . + +biolink:LogOddsAnalysisResult a sh:NodeShape ; + rdfs:subClassOf biolink:StudyResult ; + sh:closed true ; + sh:description "A result of a log odds ratio analysis." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . - -biolink:GeneToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene that is the subject of the association" ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:GeneToEntityAssociationMixin . + sh:path biolink:license ] ; + sh:targetClass biolink:LogOddsAnalysisResult . -biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; +biolink:MacromolecularComplex a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; + sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 33 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:MacromolecularComplex . + +biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:FunctionalAssociation ; + sh:closed true ; + sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 40 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:negated ], + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path rdfs:label ], + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:description "expression relationship" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:BiologicalProcess ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 36 ; - sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 21 ; - sh:path biolink:subject_closure ], + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 35 ; - sh:path biolink:category ] ; - sh:targetClass biolink:GeneToExpressionSiteAssociation . - -biolink:GeneToGeneAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . + +biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:FunctionalAssociation ; + sh:closed true ; + sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:CellularComponent ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:GeneToGeneAssociation . + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . -biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Indicates that two genes are co-expressed, generally under the same conditions." ; +biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "an association which has a macromolecular machine mixin as a subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:quantifier_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path rdf:object ] ; + sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . + +biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:FunctionalAssociation ; + sh:closed true ; + sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 32 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:original_object ], + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . + +biolink:MappingCollection a sh:NodeShape ; + sh:closed false ; + sh:description "A collection of deprecated mappings." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:PredicateMapping ; + sh:description "A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3." ; sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 0 ; + sh:path biolink:predicate_mappings ] ; + sh:targetClass biolink:MappingCollection . + +biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An association between a material sample and the material entity from which it is derived." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; - sh:path biolink:original_predicate ], + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 33 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:GeneToGeneCoexpressionAssociation . - -biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:class biolink:NamedThing ; + sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:string ; + sh:description "derivation relationship" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "a point in time" ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:GeneFamily ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "membership of the gene in the given gene family." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ] ; + sh:targetClass biolink:MaterialSampleDerivationAssociation . + +biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An association between a material sample and a disease or phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; - sh:path biolink:adjusted_p_value ] ; - sh:targetClass biolink:GeneToGeneFamilyAssociation . - -biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "homology relationship type" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:description "a point in time" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; + sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + +biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An association between a material sample and something." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ] ; - sh:targetClass biolink:GeneToGeneHomologyAssociation . + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:MaterialSample ; + sh:description "the material sample being described" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:MaterialSampleToEntityAssociationMixin . -biolink:GeneToGeneProductRelationship a sh:NodeShape ; +biolink:MicroRNA a sh:NodeShape ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; sh:closed true ; - sh:description "A gene is transcribed and potentially translated to a gene product" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:GeneProductMixin ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:MicroRNA . + +biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; + sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:NamedThing ; + sh:description "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:ModelToDiseaseAssociationMixin . + +biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; - sh:path dct:description ] ; - sh:targetClass biolink:GeneToGeneProductRelationship . - -biolink:GeneToGoTermAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . + +biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; + sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . + +biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:GeneToGoTermAssociation . - -biolink:GeneToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a gene or gene product and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:GeneToPathwayAssociation . + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; + sh:targetClass biolink:MolecularActivityToPathwayAssociation . -biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:MortalityOutcome a sh:NodeShape ; sh:closed true ; + sh:description "An outcome of death from resulting from an exposure event." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:targetClass biolink:MortalityOutcome . + +biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:population_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_total ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + sh:order 6 ; + sh:path biolink:object_context_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:PhenotypicFeature ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 4 ; sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:double ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 23 ; - sh:path biolink:object_closure ], + sh:path biolink:object_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; + sh:order 32 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 40 ; + sh:order 42 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:p_value ], + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_subject ] ; + sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . -biolink:Genome a sh:NodeShape ; +biolink:NucleicAcidSequenceMotif a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "A genome is the sum of genetic material within a cell or virion." ; + sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Genome . + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:NucleicAcidSequenceMotif . -biolink:GenomicBackgroundExposure a sh:NodeShape ; +biolink:NucleosomeModification a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; + sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 19 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_gene_or_gene_product ], + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 8 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], + sh:path biolink:id ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 3 ; + sh:order 1 ; sh:path biolink:in_taxon ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "connects a genomic feature to its sequence" ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 14 ; - sh:path biolink:synonym ], + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 12 ; - sh:path biolink:xref ], + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:GenomicBackgroundExposure . - -biolink:GenomicEntity a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; - sh:targetClass biolink:GenomicEntity . + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:NucleosomeModification . -biolink:GenomicSequenceLocalization a sh:NodeShape ; +biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; + rdfs:subClassOf biolink:StudyResult ; sh:closed true ; - sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; + sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 37 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path rdf:object ], + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 39 ; - sh:path rdf:type ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:start_interbase_coordinate ], + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:description "The strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand)." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:strand ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ] ; + sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . + +biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "An association between an organism taxon and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:end_interbase_coordinate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 36 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:OrganismTaxonToEntityAssociation . + +biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:NamedThing ; + sh:description "the environment in which the organism occurs" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 35 ; + sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 43 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - sh:in ( "+" "-" "." "?" ) ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:genome_build ] ; - sh:targetClass biolink:GenomicSequenceLocalization . - -biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . + +biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + sh:closed true ; + sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:associated_environmental_context ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:id ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 7 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 28 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; sh:path biolink:p_value ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:object ], + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 13 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 38 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; + sh:order 8 ; sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 23 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . + +biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + sh:closed true ; + sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . - -biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Genotype ; - sh:description "a genotype that is associated in some way with a disease state" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . + +biolink:OrganismToOrganismAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "E.g. is pathogenic for" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:IndividualOrganism ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that genotype" ; + [ sh:class biolink:IndividualOrganism ; + sh:description "An association between two individual organisms." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ] ; - sh:targetClass biolink:GenotypeToDiseaseAssociation . - -biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Genotype ; - sh:description "genotype that is the subject of the association" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ] ; - sh:targetClass biolink:GenotypeToEntityAssociationMixin . + sh:targetClass biolink:OrganismToOrganismAssociation . -biolink:GenotypeToGeneAssociation a sh:NodeShape ; +biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "the relationship type used to connect genotype to gene" ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Gene ; - sh:description "gene implicated in genotype" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:GenotypeToGeneAssociation . - -biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:path biolink:deprecated ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OrganismalEntity ; + sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:Genotype ; - sh:description "child genotype" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ] ; + sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + +biolink:PairwiseMolecularInteraction a sh:NodeShape ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + sh:closed true ; + sh:description "An interaction at the molecular level between two physical entities" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; + sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:GenotypeToGenotypePartAssociation . - -biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:MolecularEntity ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 3 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_supporting_studies ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . - -biolink:GenotypeToVariantAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Any association between a genotype and a sequence variant." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:MolecularEntity ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "a point in time" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "interaction relationship type" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ] ; + sh:targetClass biolink:PairwiseMolecularInteraction . + +biolink:Patent a sh:NodeShape ; + rdfs:subClassOf biolink:Publication ; + sh:closed true ; + sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; sh:path dct:description ], - [ sh:description "the relationship type used to connect genotype to gene" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:object_category ], + sh:path rdfs:label ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:object ], + sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:GenotypeToVariantAssociation . + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Patent . -biolink:GenotypicSex a sh:NodeShape ; +biolink:PathognomonicityQuantifier a sh:NodeShape ; + rdfs:subClassOf biolink:SpecificityQuantifier ; + sh:closed false ; + sh:description "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PathognomonicityQuantifier . + +biolink:PathologicalAnatomicalExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; + sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; + sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; + sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ] ; - sh:targetClass biolink:GenotypicSex . + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:PathologicalAnatomicalExposure . -biolink:GeographicExposure a sh:NodeShape ; +biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; sh:closed true ; - sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; + sh:description "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PathologicalAnatomicalOutcome . + +biolink:PathologicalAnatomicalStructure a sh:NodeShape ; + rdfs:subClassOf biolink:AnatomicalEntity ; + sh:closed true ; + sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:order 12 ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path rdf:type ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:PathologicalAnatomicalStructure . + +biolink:PathologicalEntityMixin a sh:NodeShape ; + sh:closed false ; + sh:description "A pathological (abnormal) structure or process." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PathologicalEntityMixin . + +biolink:PathologicalProcess a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalProcess ; + sh:closed true ; + sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GeographicExposure . - -biolink:GeographicLocation a sh:NodeShape ; - sh:closed true ; - sh:description "a location that can be described in lat/long coordinates" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:latitude ], + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:longitude ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:GeographicLocation . - -biolink:GeographicLocationAtTime a sh:NodeShape ; - sh:closed true ; - sh:description "a location that can be described in lat/long coordinates, for a particular time" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "longitude" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:longitude ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; sh:path dct:description ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "a point in time" ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:latitude ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GeographicLocationAtTime . + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:PathologicalProcess . -biolink:GrossAnatomicalStructure a sh:NodeShape ; +biolink:PathologicalProcessExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; + sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:category ] ; - sh:targetClass biolink:GrossAnatomicalStructure . + sh:targetClass biolink:PathologicalProcessExposure . -biolink:Haplotype a sh:NodeShape ; +biolink:PathologicalProcessOutcome a sh:NodeShape ; sh:closed true ; - sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; + sh:description "An outcome resulting from an exposure event which is the manifestation of a pathological process." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:targetClass biolink:PathologicalProcessOutcome . + +biolink:Phenomenon a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed true ; + sh:description "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:xref ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:id ] ; - sh:targetClass biolink:Haplotype . + sh:targetClass biolink:Phenomenon . -biolink:Hospitalization a sh:NodeShape ; +biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Hospitalization . - -biolink:HospitalizationOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:HospitalizationOutcome . - -biolink:Human a sh:NodeShape ; - sh:closed true ; - sh:description "A member of the the species Homo sapiens." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:Human . - -biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:timepoint ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 3 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 29 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:path biolink:subject_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 7 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; + sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "a point in time" ; + sh:order 23 ; + sh:path biolink:object_category_closure ] ; + sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . + +biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; + rdfs:subClassOf biolink:FeatureOrDiseaseQualifiersToEntityMixin ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:has_quotient ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . - -biolink:Invertebrate a sh:NodeShape ; - sh:closed true ; - sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdf:object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_total ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Invertebrate . + sh:order 6 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_count ] ; + sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . -biolink:JournalArticle a sh:NodeShape ; +biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; + sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:creation_date ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 10 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 7 ; - sh:path biolink:keywords ], + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:license ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:category ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; sh:order 22 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 17 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path dct:description ], + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 5 ; - sh:path biolink:pages ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:issue ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:order 21 ; - sh:path rdf:type ], - [ sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:published_in ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:summary ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 8 ; - sh:path biolink:mesh_terms ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:qualifiers ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:rights ], + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 24 ; + sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 15 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:JournalArticle . - -biolink:LogOddsAnalysisResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of a log odds ratio analysis." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ] ; - sh:targetClass biolink:LogOddsAnalysisResult . + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . -biolink:MacromolecularComplex a sh:NodeShape ; +biolink:PhenotypicQuality a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismAttribute ; sh:closed true ; - sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; + sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path rdf:type ], + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:MacromolecularComplex . - -biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:iri ] ; + sh:targetClass biolink:PhenotypicQuality . + +biolink:PhenotypicSex a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalSex ; + sh:closed true ; + sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:BiologicalProcess ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; + sh:targetClass biolink:PhenotypicSex . + +biolink:PhysicalEssence a sh:NodeShape ; + rdfs:subClassOf biolink:PhysicalEssenceOrOccurrent ; + sh:closed false ; + sh:description "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PhysicalEssence . + +biolink:PhysiologicalProcess a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalProcess ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ] ; - sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . - -biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:negated ], + sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:PhysiologicalProcess . + +biolink:Plant a sh:NodeShape ; + rdfs:subClassOf biolink:CellularOrganism ; + sh:closed true ; + sh:description "" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:CellularComponent ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:Plant . + +biolink:PopulationToPopulationAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An association between a two populations" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -17714,2087 +22310,2000 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ] ; - sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . - -biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "an association which has a macromolecular machine mixin as a subject" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . - -biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the object of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:PopulationToPopulationAssociation . -biolink:Mammal a sh:NodeShape ; +biolink:PosttranslationalModification a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; + sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:Mammal . - -biolink:MappingCollection a sh:NodeShape ; - sh:closed false ; - sh:description "A collection of deprecated mappings." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PredicateMapping ; - sh:description "A collection of relationships that are not used in biolink, but have biolink patterns that can be used to replace them. This is a temporary slot to help with the transition to the fully qualified predicate model in Biolink3." ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:predicate_mappings ] ; - sh:targetClass biolink:MappingCollection . - -biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a material sample and the material entity from which it is derived." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:PosttranslationalModification . + +biolink:PreprintPublication a sh:NodeShape ; + rdfs:subClassOf biolink:Publication ; + sh:closed true ; + sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:id ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:path biolink:format ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "derivation relationship" ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; - sh:targetClass biolink:MaterialSampleDerivationAssociation . + sh:order 20 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:PreprintPublication . -biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "An association between a material sample and a disease or phenotype." ; + sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ] ; - sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . - -biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "An association between a material sample and something." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:MaterialSample ; - sh:description "the material sample being described" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:MaterialSampleToEntityAssociationMixin . - -biolink:MicroRNA a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:MicroRNA . - -biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; - sh:closed false ; - sh:description "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The relationship to the disease" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:BiologicalProcess ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:NamedThing ; - sh:description "The entity that serves as the model of the disease. This may be an organism, a strain of organism, a genotype or variant that exhibits similar features, or a gene that when mutated exhibits features of the disease" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:ModelToDiseaseAssociationMixin . - -biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:MolecularActivity ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:BiologicalProcess ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:path biolink:has_supporting_studies ] ; + sh:targetClass biolink:ProcessRegulatesProcessAssociation . + +biolink:ProcessedMaterial a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalMixture ; + sh:closed true ; + sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ProcessedMaterial . + +biolink:ProteinDomain a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ] ; - sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ] ; + sh:targetClass biolink:ProteinDomain . -biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; +biolink:ProteinFamily a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:id ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; + sh:order 13 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:ProteinFamily . + +biolink:ProteinIsoform a sh:NodeShape ; + rdfs:subClassOf biolink:Protein ; + sh:closed true ; + sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:ProteinIsoform . + +biolink:RNAProductIsoform a sh:NodeShape ; + rdfs:subClassOf biolink:RNAProduct ; + sh:closed true ; + sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:RNAProductIsoform . -biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; +biolink:ReactionToCatalystAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; sh:closed true ; - sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 40 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 8 ; sh:path biolink:qualifiers ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:original_subject ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:path biolink:agent_type ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReagentTargetedGene a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; - sh:targetClass biolink:MolecularActivityToPathwayAssociation . - -biolink:MolecularMixture a sh:NodeShape ; - sh:closed true ; - sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 13 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:xref ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ] ; - sh:targetClass biolink:MolecularMixture . + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:ReagentTargetedGene . -biolink:MortalityOutcome a sh:NodeShape ; +biolink:RelationshipType a sh:NodeShape ; + rdfs:subClassOf biolink:OntologyClass ; sh:closed true ; - sh:description "An outcome of death from resulting from an exposure event." ; + sh:description "An OWL property used as an edge label" ; sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:MortalityOutcome . + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:RelationshipType . -biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape ; +biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; + rdfs:subClassOf biolink:StudyResult ; sh:closed true ; - sh:description "" ; + sh:description "A result of a relative frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:object_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 36 ; - sh:path biolink:id ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ] ; + sh:targetClass biolink:RelativeFrequencyAnalysisResult . + +biolink:SensitivityQuantifier a sh:NodeShape ; + rdfs:subClassOf biolink:RelationshipQuantifier ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SensitivityQuantifier . + +biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed false ; + sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 11 ; + sh:order 6 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 39 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path dct:description ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], + sh:path biolink:knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:population_context_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_aspect_qualifier ] ; - sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . - -biolink:NoncodingRNAProduct a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:order 9 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:NoncodingRNAProduct . + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . -biolink:NucleicAcidSequenceMotif a sh:NodeShape ; +biolink:Serial a sh:NodeShape ; + rdfs:subClassOf biolink:Publication ; sh:closed true ; - sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; + sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:format ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 23 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:issue ], + [ sh:datatype xsd:string ; + sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:iso_abbreviation ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:NucleicAcidSequenceMotif . - -biolink:NucleosomeModification a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:path biolink:volume ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:rights ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 3 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:id ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:NucleosomeModification . - -biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of a observed expected frequency analysis." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 11 ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; sh:path rdf:type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:license ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ] ; - sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . - -biolink:Occurrent a sh:NodeShape ; - sh:closed false ; - sh:description "A processual entity." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:Occurrent . + sh:path biolink:xref ] ; + sh:targetClass biolink:Serial . -biolink:OrganismAttribute a sh:NodeShape ; +biolink:SeverityValue a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "describes a characteristic of an organismal entity." ; + sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -19802,1263 +24311,1385 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ] ; + sh:targetClass biolink:SeverityValue . + +biolink:SiRNA a sh:NodeShape ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; + sh:closed true ; + sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:OrganismAttribute . - -biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "An association between an organism taxon and another entity" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:OrganismTaxonToEntityAssociation . + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ] ; + sh:targetClass biolink:SiRNA . -biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; - sh:closed false ; +biolink:SmallMolecule a sh:NodeShape ; + rdfs:subClassOf biolink:MolecularEntity ; + sh:closed true ; + sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:NamedThing ; - sh:description "the environment in which the organism occurs" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:path biolink:is_metabolite ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "predicate describing the relationship between the taxon and the environment" ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:SmallMolecule . + +biolink:Snv a sh:NodeShape ; + rdfs:subClassOf biolink:SequenceVariant ; + sh:closed true ; + sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 0 ; + sh:path biolink:has_gene ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ] ; - sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . + sh:order 14 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:Snv . -biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "A relationship between two organism taxon nodes" ; +biolink:SocioeconomicExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; + sh:closed true ; + sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:SocioeconomicAttribute ; sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ] ; + sh:targetClass biolink:SocioeconomicExposure . + +biolink:SocioeconomicOutcome a sh:NodeShape ; + sh:closed true ; + sh:description "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SocioeconomicOutcome . + +biolink:StudyVariable a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; + sh:closed true ; + sh:description "a variable that is used as a measure in the investigation of a study" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:has_evidence ], + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:StudyVariable . -biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; +biolink:SubjectOfInvestigation a sh:NodeShape ; + sh:closed false ; + sh:description "An entity that has the role of being studied in an investigation, study, or experiment" ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SubjectOfInvestigation . + +biolink:TaxonToTaxonAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; + sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 25 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:timepoint ], + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "the environment in which the two taxa interact" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 17 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:TaxonToTaxonAssociation . -biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; +biolink:TextMiningResult a sh:NodeShape ; + rdfs:subClassOf biolink:StudyResult ; sh:closed true ; - sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; + sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ] ; + sh:targetClass biolink:TextMiningResult . + +biolink:ThingWithTaxon a sh:NodeShape ; + sh:closed false ; + sh:description "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:ThingWithTaxon . + +biolink:TranscriptToGeneRelationship a sh:NodeShape ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; + sh:closed true ; + sh:description "A gene is a collection of transcripts" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a point in time" ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Transcript ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . - -biolink:OrganismToOrganismAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:IndividualOrganism ; - sh:description "An association between two individual organisms." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ] ; + sh:targetClass biolink:TranscriptToGeneRelationship . + +biolink:TranscriptionFactorBindingSite a sh:NodeShape ; + rdfs:subClassOf biolink:RegulatoryRegion ; + sh:closed true ; + sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ] ; - sh:targetClass biolink:OrganismToOrganismAssociation . + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:TranscriptionFactorBindingSite . -biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; +biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "The relationship to the disease" ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OrganismalEntity ; - sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 40 ; sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -21072,4364 +25703,5126 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 42 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ] ; - sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ] ; + sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . -biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; +biolink:VariantToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; + sh:targetClass biolink:VariantToEntityAssociationMixin . + +biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; sh:closed true ; - sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; + sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "a point in time" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 13 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "interaction relationship type" ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; + sh:order 26 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:expression_site ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 3 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:PairwiseGeneToGeneInteraction . - -biolink:PairwiseMolecularInteraction a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction at the molecular level between two physical entities" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ] ; + sh:targetClass biolink:VariantToGeneExpressionAssociation . + +biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:class biolink:MolecularEntity ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "interaction relationship type" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:class biolink:MolecularEntity ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; + sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:PairwiseMolecularInteraction . - -biolink:Patent a sh:NodeShape ; - sh:closed true ; - sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 17 ; - sh:path rdf:type ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:path biolink:original_object ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ] ; - sh:targetClass biolink:Patent . - -biolink:PathognomonicityQuantifier a sh:NodeShape ; - sh:closed false ; - sh:description "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PathognomonicityQuantifier . - -biolink:PathologicalAnatomicalExposure a sh:NodeShape ; - sh:closed true ; - sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:PathologicalAnatomicalExposure . - -biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PathologicalAnatomicalOutcome . + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . -biolink:PathologicalAnatomicalStructure a sh:NodeShape ; +biolink:VariantToPopulationAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; + sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:integer ; + sh:description "number all populations that carry a particular allele, aka allele number" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_total ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:has_evidence ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:has_percentage ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:PathologicalAnatomicalStructure . - -biolink:PathologicalEntityMixin a sh:NodeShape ; - sh:closed false ; - sh:description "A pathological (abnormal) structure or process." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PathologicalEntityMixin . - -biolink:PathologicalProcess a sh:NodeShape ; - sh:closed true ; - sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + sh:order 11 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:order 12 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; sh:order 16 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:PathologicalProcess . - -biolink:PathologicalProcessExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:order 22 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 42 ; sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:integer ; + sh:description "number in object population that carry a particular allele, aka allele count" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:double ; + sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:PathologicalProcessExposure . - -biolink:PathologicalProcessOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An outcome resulting from an exposure event which is the manifestation of a pathological process." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PathologicalProcessOutcome . + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_subject ] ; + sh:targetClass biolink:VariantToPopulationAssociation . -biolink:Phenomenon a sh:NodeShape ; +biolink:Vertebrate a sh:NodeShape ; + rdfs:subClassOf biolink:CellularOrganism ; sh:closed true ; - sh:description "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; + sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:category ], + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path dct:description ] ; - sh:targetClass biolink:Phenomenon . + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:Vertebrate . -biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; +biolink:Virus a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismalEntity ; sh:closed true ; + sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 37 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:Virus . + +biolink:WebPage a sh:NodeShape ; + rdfs:subClassOf biolink:Publication ; + sh:closed true ; + sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:double ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:Disease ; - sh:description "disease" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path rdf:object ], + sh:path biolink:keywords ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:path biolink:pages ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; + sh:order 20 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:WebPage . + +biolink:Activity a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed true ; + sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; - sh:path biolink:id ] ; - sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ] ; + sh:targetClass biolink:Activity . -biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; +biolink:AdministrativeEntity a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path rdf:predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path rdf:object ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_quotient ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; sh:order 10 ; - sh:path biolink:frequency_qualifier ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_total ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path rdf:subject ] ; - sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . - -biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], + sh:path biolink:deprecated ] ; + sh:targetClass biolink:AdministrativeEntity . + +biolink:Annotation a sh:NodeShape ; + sh:closed false ; + sh:description "Biolink Model root class for entity annotations." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:Annotation . + +biolink:Article a sh:NodeShape ; + rdfs:subClassOf biolink:Publication ; + sh:closed true ; + sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:issue ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:summary ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:double ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path dct:type ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:full_name ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:iri ], + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:volume ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; sh:path biolink:deprecated ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], + sh:order 24 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:xref ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:category ] ; + sh:targetClass biolink:Article . + +biolink:Behavior a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalProcess ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:original_predicate ], + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:Behavior . + +biolink:BehavioralFeature a sh:NodeShape ; + rdfs:subClassOf biolink:PhenotypicFeature ; + sh:closed true ; + sh:description "A phenotypic feature which is behavioral in nature." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; + sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; - sh:path rdf:type ] ; - sh:targetClass biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . - -biolink:PhenotypicQuality a sh:NodeShape ; - sh:closed true ; - sh:description "A property of a phenotype" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:category ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:BehavioralFeature . + +biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:order 5 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:PhenotypicQuality . - -biolink:PhenotypicSex a sh:NodeShape ; - sh:closed true ; - sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:PhenotypicSex . - -biolink:PhysicalEssence a sh:NodeShape ; - sh:closed false ; - sh:description "Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PhysicalEssence . - -biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; - sh:closed false ; - sh:description "Either a physical or processual entity." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:PhysicalEssenceOrOccurrent . - -biolink:PhysiologicalProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_output ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ] ; - sh:targetClass biolink:PhysiologicalProcess . + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . -biolink:PlanetaryEntity a sh:NodeShape ; +biolink:CellularComponent a sh:NodeShape ; + rdfs:subClassOf biolink:AnatomicalEntity ; sh:closed true ; - sh:description "Any entity or process that exists at the level of the whole planet" ; + sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:xref ], + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path rdf:type ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ] ; - sh:targetClass biolink:PlanetaryEntity . - -biolink:Plant a sh:NodeShape ; - sh:closed true ; - sh:description "" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:CellularComponent . + +biolink:ChemicalExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; + sh:closed true ; + sh:description "A chemical exposure is an intake of a particular chemical entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path rdfs:label ], + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:Plant . - -biolink:Polypeptide a sh:NodeShape ; - sh:closed true ; - sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:Polypeptide . + sh:path dct:description ] ; + sh:targetClass biolink:ChemicalExposure . -biolink:PopulationToPopulationAssociation a sh:NodeShape ; +biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "An association between a two populations" ; + sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the object of the association" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 18 ; sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 6 ; + sh:order 7 ; sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + +biolink:ClinicalCourse a sh:NodeShape ; + rdfs:subClassOf biolink:ClinicalAttribute ; + sh:closed true ; + sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "a point in time" ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:ClinicalCourse . + +biolink:ClinicalIntervention a sh:NodeShape ; + rdfs:subClassOf biolink:ClinicalEntity ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:has_evidence ], + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:PopulationToPopulationAssociation . + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ] ; + sh:targetClass biolink:ClinicalIntervention . -biolink:PosttranslationalModification a sh:NodeShape ; +biolink:Dataset a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; sh:closed true ; - sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; + sh:description "an item that refers to a collection of data from a data source." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:PosttranslationalModification . + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ] ; + sh:targetClass biolink:Dataset . -biolink:PreprintPublication a sh:NodeShape ; +biolink:DatasetDistribution a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; sh:closed true ; - sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; + sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:full_name ], + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 15 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:distribution_download_url ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; sh:path biolink:license ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:iri ], - [ sh:description "mesh terms tagging a publication" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:DatasetDistribution . + +biolink:Device a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed true ; + sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 19 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ] ; - sh:targetClass biolink:PreprintPublication . + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ] ; + sh:targetClass biolink:Device . -biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; +biolink:DrugExposure a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalExposure ; sh:closed true ; - sh:description "Describes a regulatory relationship between two genes or gene products." ; + sh:description "A drug exposure is an intake of a particular drug." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:DrugExposure . + +biolink:EnvironmentalExposure a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; + sh:closed true ; + sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:publications ], + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:EnvironmentalExposure . + +biolink:Exon a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path rdf:type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 35 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ] ; - sh:targetClass biolink:ProcessRegulatesProcessAssociation . + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:Exon . -biolink:ProcessedMaterial a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; +biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; + rdfs:subClassOf biolink:FrequencyQualifierMixin ; + sh:closed false ; + sh:description "Qualifiers for disease or phenotype to entity associations." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:id ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ] ; + sh:targetClass biolink:FeatureOrDiseaseQualifiersToEntityMixin . + +biolink:GeneFamily a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:description "any grouping of multiple genes or gene products related by common descent" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 10 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:is_supplement ] ; - sh:targetClass biolink:ProcessedMaterial . + sh:path biolink:has_gene_or_gene_product ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ] ; + sh:targetClass biolink:GeneFamily . -biolink:Protein a sh:NodeShape ; +biolink:GeneticInheritance a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; + sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Protein . + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:GeneticInheritance . -biolink:ProteinDomain a sh:NodeShape ; +biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Genotype ; + sh:description "a genotype that is associated in some way with a disease state" ; sh:maxCount 1 ; - sh:order 8 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ] ; - sh:targetClass biolink:ProteinDomain . - -biolink:ProteinFamily a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:order 5 ; - sh:path biolink:full_name ], + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ] ; - sh:targetClass biolink:ProteinFamily . - -biolink:ProteinIsoform a sh:NodeShape ; - sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:path biolink:timepoint ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:in_taxon ], + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "E.g. is pathogenic for" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:ProteinIsoform . + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ] ; + sh:targetClass biolink:GenotypeToDiseaseAssociation . -biolink:RNAProduct a sh:NodeShape ; +biolink:GeographicLocation a sh:NodeShape ; + rdfs:subClassOf biolink:PlanetaryEntity ; sh:closed true ; + sh:description "a location that can be described in lat/long coordinates" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "longitude" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:longitude ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:RNAProduct . - -biolink:RNAProductIsoform a sh:NodeShape ; - sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:float ; + sh:description "latitude" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:latitude ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:GeographicLocation . + +biolink:Mammal a sh:NodeShape ; + rdfs:subClassOf biolink:CellularOrganism ; + sh:closed true ; + sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; - sh:targetClass biolink:RNAProductIsoform . - -biolink:ReactionToCatalystAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:category ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path rdf:subject ], + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:Mammal . + +biolink:MolecularMixture a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalMixture ; + sh:closed true ; + sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; sh:path dct:description ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 37 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ] ; + sh:targetClass biolink:MolecularMixture . + +biolink:Occurrent a sh:NodeShape ; + rdfs:subClassOf biolink:PhysicalEssenceOrOccurrent ; + sh:closed false ; + sh:description "A processual entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:Occurrent . + +biolink:Onset a sh:NodeShape ; + rdfs:subClassOf biolink:ClinicalCourse ; + sh:closed true ; + sh:description "The age group in which (disease) symptom manifestations appear." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; + sh:targetClass biolink:Onset . + +biolink:OrganismAttribute a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; + sh:closed true ; + sh:description "describes a characteristic of an organismal entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 40 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path rdf:predicate ], + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 41 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:OrganismAttribute . + +biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; + sh:closed true ; + sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:ReactionToParticipantAssociation . - -biolink:ReagentTargetedGene a sh:NodeShape ; - sh:closed true ; - sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "connects a genomic feature to its sequence" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:order 10 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ReagentTargetedGene . - -biolink:RegulatoryRegion a sh:NodeShape ; - sh:closed true ; - sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "interaction relationship type" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:id ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 12 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:RegulatoryRegion . - -biolink:RelationshipQuantifier a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:RelationshipQuantifier . - -biolink:RelationshipType a sh:NodeShape ; - sh:closed true ; - sh:description "An OWL property used as an edge label" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ] ; - sh:targetClass biolink:RelationshipType . + sh:order 11 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:PairwiseGeneToGeneInteraction . -biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; +biolink:Polypeptide a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "A result of a relative frequency analysis." ; + sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:category ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 11 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:RelativeFrequencyAnalysisResult . - -biolink:SensitivityQuantifier a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SensitivityQuantifier . + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ] ; + sh:targetClass biolink:Polypeptide . -biolink:SequenceAssociation a sh:NodeShape ; +biolink:PredicateMapping a sh:NodeShape ; sh:closed true ; - sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; + sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 17 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:exact_match ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:path biolink:object_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:path biolink:mapped_predicate ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:broad_match ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:object_context_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 19 ; + sh:path biolink:narrow_match ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 2 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ] ; + sh:targetClass biolink:PredicateMapping . + +biolink:Procedure a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed true ; + sh:description "A series of actions conducted in a certain order or manner" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:object ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; - sh:targetClass biolink:SequenceAssociation . + sh:path biolink:iri ] ; + sh:targetClass biolink:Procedure . -biolink:SequenceFeatureRelationship a sh:NodeShape ; +biolink:Protein a sh:NodeShape ; + rdfs:subClassOf biolink:Polypeptide ; sh:closed true ; - sh:description "For example, a particular exon is part of a particular transcript or gene" ; + sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:publications ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:Protein . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; + sh:order 20 ; sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; sh:path rdf:type ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:stoichiometry ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 40 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:SequenceFeatureRelationship . - -biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path rdf:predicate ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path biolink:object_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:ReactionToParticipantAssociation . + +biolink:SequenceAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . - -biolink:Serial a sh:NodeShape ; - sh:closed true ; - sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 23 ; + sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 9 ; - sh:path dct:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 22 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 16 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:order 20 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:issue ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 7 ; - sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:license ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:iri ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:summary ], + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:volume ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 4 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 6 ; - sh:path biolink:keywords ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:rights ] ; - sh:targetClass biolink:Serial . + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ] ; + sh:targetClass biolink:SequenceAssociation . -biolink:SeverityValue a sh:NodeShape ; +biolink:SocioeconomicAttribute a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "describes the severity of a phenotypic feature or disease" ; + sh:description "Attributes relating to a socioeconomic manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -25438,554 +30831,619 @@ biolink:SeverityValue a sh:NodeShape ; sh:order 1 ; sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:SeverityValue . - -biolink:SiRNA a sh:NodeShape ; - sh:closed true ; - sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; sh:order 13 ; - sh:path biolink:deprecated ], + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:SocioeconomicAttribute . + +biolink:SpecificityQuantifier a sh:NodeShape ; + rdfs:subClassOf biolink:RelationshipQuantifier ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:SpecificityQuantifier . + +biolink:StudyPopulation a sh:NodeShape ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; + sh:closed true ; + sh:description "A group of people banded together or treated as a group as participants in a research study." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:SiRNA . - -biolink:SmallMolecule a sh:NodeShape ; - sh:closed true ; - sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:trade_name ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:is_metabolite ], + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:SmallMolecule . + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:StudyPopulation . -biolink:Snv a sh:NodeShape ; +biolink:TaxonomicRank a sh:NodeShape ; + rdfs:subClassOf biolink:OntologyClass ; sh:closed true ; - sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; + sh:description "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:boolean ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ] ; + sh:targetClass biolink:TaxonomicRank . + +biolink:Treatment a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed true ; + sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + [ sh:class biolink:Device ; + sh:description "connects an entity to one or more (medical) devices" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_device ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:timepoint ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 2 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:Snv . + [ sh:class biolink:Drug ; + sh:description "connects an entity to one or more drugs" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_drug ], + [ sh:class biolink:Procedure ; + sh:description "connects an entity to one or more (medical) procedures" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_procedure ] ; + sh:targetClass biolink:Treatment . -biolink:SocioeconomicExposure a sh:NodeShape ; +biolink:VariantToDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:SocioeconomicAttribute ; - sh:description "connects any entity to an attribute" ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path rdfs:label ], + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:order 12 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 7 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:SocioeconomicExposure . - -biolink:SocioeconomicOutcome a sh:NodeShape ; - sh:closed true ; - sh:description "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SocioeconomicOutcome . - -biolink:SpecificityQuantifier a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SpecificityQuantifier . - -biolink:StudyPopulation a sh:NodeShape ; - sh:closed true ; - sh:description "A group of people banded together or treated as a group as participants in a research study." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:StudyPopulation . - -biolink:StudyResult a sh:NodeShape ; - sh:closed false ; - sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:id ], + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:StudyResult . + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; + sh:targetClass biolink:VariantToDiseaseAssociation . -biolink:StudyVariable a sh:NodeShape ; +biolink:VariantToGeneAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "a variable that is used as a measure in the investigation of a study" ; + sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:order 0 ; - sh:path biolink:license ], + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:order 11 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:xref ], + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ] ; - sh:targetClass biolink:StudyVariable . - -biolink:SubjectOfInvestigation a sh:NodeShape ; - sh:closed false ; - sh:description "An entity that has the role of being studied in an investigation, study, or experiment" ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:SubjectOfInvestigation . - -biolink:TaxonToTaxonAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; @@ -25993,1928 +31451,2414 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:TaxonToTaxonAssociation . + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; + sh:targetClass biolink:VariantToGeneAssociation . -biolink:TextMiningResult a sh:NodeShape ; +biolink:Zygosity a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "a long-form human readable name for a thing" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ] ; - sh:targetClass biolink:TextMiningResult . + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:Zygosity . -biolink:ThingWithTaxon a sh:NodeShape ; +biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed false ; - sh:description "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:ThingWithTaxon . - -biolink:TranscriptToGeneRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A gene is a collection of transcripts" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Transcript ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:AnatomicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; - sh:targetClass biolink:TranscriptToGeneRelationship . + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . -biolink:TranscriptionFactorBindingSite a sh:NodeShape ; +biolink:BiologicalProcessOrActivity a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; + sh:description "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:property [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 3 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:TranscriptionFactorBindingSite . + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:id ] ; + sh:targetClass biolink:BiologicalProcessOrActivity . -biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; +biolink:Case a sh:NodeShape ; + rdfs:subClassOf biolink:IndividualOrganism ; sh:closed true ; + sh:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:qualifier ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 36 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path dct:description ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:Case . + +biolink:CellLine a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismalEntity ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "The relationship to the disease" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; + sh:targetClass biolink:CellLine . + +biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; + sh:closed false ; + sh:description "An interaction between a chemical entity and another entity" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . + +biolink:ChemicalToChemicalAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ] ; - sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . - -biolink:VariantToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:ChemicalToChemicalAssociation . + +biolink:ClinicalEntity a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed true ; + sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:ClinicalEntity . + +biolink:Entity a sh:NodeShape ; + sh:closed false ; + sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdf:object ], + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 37 ; + sh:order 6 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path dct:description ] ; + sh:targetClass biolink:Entity . + +biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; + rdfs:subClassOf biolink:FrequencyQualifierMixin ; + sh:closed false ; + sh:description "Qualifiers for entity to disease or phenotype associations." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; - sh:path biolink:publications ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "E.g. is pathogenic for" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:p_value ] ; - sh:targetClass biolink:VariantToDiseaseAssociation . + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ] ; + sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . -biolink:VariantToEntityAssociationMixin a sh:NodeShape ; +biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:closed false ; + sh:description "Qualifier for frequency type associations" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; + sh:order 3 ; sh:path rdf:object ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path rdf:predicate ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:order 1 ; sh:path rdf:subject ] ; - sh:targetClass biolink:VariantToEntityAssociationMixin . + sh:targetClass biolink:FrequencyQualifierMixin . -biolink:VariantToGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; +biolink:GeneProductMixin a sh:NodeShape ; + rdfs:subClassOf biolink:GeneOrGeneProduct ; + sh:closed false ; + sh:description "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:GeneProductMixin . + +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 34 ; - sh:path rdf:type ], + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 28 ; - sh:path biolink:p_value ], + sh:path biolink:subject_label_closure ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; + sh:order 30 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 38 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 15 ; sh:path biolink:agent_type ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 35 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; sh:order 37 ; - sh:path biolink:has_attribute ], + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 23 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 31 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; - sh:targetClass biolink:VariantToGeneAssociation . + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ] ; + sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . -biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; +biolink:NoncodingRNAProduct a sh:NodeShape ; + rdfs:subClassOf biolink:RNAProduct ; sh:closed true ; - sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path rdf:predicate ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:NoncodingRNAProduct . + +biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed false ; + sh:description "A relationship between two organism taxon nodes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 41 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; + sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 38 ; - sh:path rdf:type ], + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 37 ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 42 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 35 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 39 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 11 ; + sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; + sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:description "a point in time" ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:original_subject ] ; - sh:targetClass biolink:VariantToGeneExpressionAssociation . + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . -biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; +biolink:Outcome a sh:NodeShape ; + sh:closed false ; + sh:description "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:Outcome . + +biolink:PhysicalEssenceOrOccurrent a sh:NodeShape ; + sh:closed false ; + sh:description "Either a physical or processual entity." ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:PhysicalEssenceOrOccurrent . + +biolink:RNAProduct a sh:NodeShape ; + rdfs:subClassOf biolink:Transcript ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:description "a point in time" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 35 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 32 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:RNAProduct . + +biolink:RegulatoryRegion a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 33 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path biolink:has_total ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:has_count ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:RegulatoryRegion . + +biolink:Drug a sh:NodeShape ; + rdfs:subClassOf biolink:MolecularMixture ; + sh:closed true ; + sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 4 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:is_supplement ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:agent_type ] ; - sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . - -biolink:VariantToPopulationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "number in object population that carry a particular allele, aka allele count" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:double ; - sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:order 39 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ] ; + sh:targetClass biolink:Drug . + +biolink:ExposureEvent a sh:NodeShape ; + rdfs:subClassOf biolink:OntologyClass ; + sh:closed false ; + sh:description "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ] ; + sh:targetClass biolink:ExposureEvent . + +biolink:GeneToGeneAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; + sh:closed false ; + sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 28 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that is observed to have the frequency" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 11 ; + sh:order 6 ; sh:path biolink:publications ], - [ sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:integer ; - sh:description "number all populations that carry a particular allele, aka allele number" ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:has_total ], - [ sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 19 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 21 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 17 ; + sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:has_percentage ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 41 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:defaultValue "not_provided" ; - sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:order 38 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 29 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 25 ; - sh:path biolink:object_closure ], + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 36 ; - sh:path biolink:id ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 37 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:VariantToPopulationAssociation . + sh:order 7 ; + sh:path biolink:has_evidence ] ; + sh:targetClass biolink:GeneToGeneAssociation . -biolink:Vertebrate a sh:NodeShape ; +biolink:IndividualOrganism a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismalEntity ; sh:closed true ; - sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; + sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; @@ -27924,2889 +33868,3201 @@ biolink:Vertebrate a sh:NodeShape ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:Vertebrate . + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; + sh:targetClass biolink:IndividualOrganism . -biolink:Virus a sh:NodeShape ; +biolink:MaterialSample a sh:NodeShape ; + rdfs:subClassOf biolink:PhysicalEntity ; sh:closed true ; - sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; + sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:Virus . + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ] ; + sh:targetClass biolink:MaterialSample . -biolink:WebPage a sh:NodeShape ; +biolink:Pathway a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalProcess ; sh:closed true ; - sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:synonym ], - [ sh:description "mesh terms tagging a publication" ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:Pathway . + +biolink:PlanetaryEntity a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed true ; + sh:description "Any entity or process that exists at the level of the whole planet" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:keywords ], + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; + sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:rights ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 21 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:category ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 18 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:WebPage . + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:PlanetaryEntity . -biolink:Behavior a sh:NodeShape ; +biolink:RelationshipQuantifier a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:targetClass biolink:RelationshipQuantifier . + +biolink:SequenceFeatureRelationship a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; + sh:description "For example, a particular exon is part of a particular transcript or gene" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:order 12 ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ] ; - sh:targetClass biolink:Behavior . - -biolink:BehavioralFeature a sh:NodeShape ; - sh:closed true ; - sh:description "A phenotypic feature which is behavioral in nature." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:deprecated ], + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:BehavioralFeature . - -biolink:CellularComponent a sh:NodeShape ; - sh:closed true ; - sh:description "A location in or around a cell" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:CellularComponent . + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:SequenceFeatureRelationship . -biolink:ClinicalAttribute a sh:NodeShape ; +biolink:Transcript a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "Attributes relating to a clinical manifestation" ; + sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:ClinicalAttribute . - -biolink:Dataset a sh:NodeShape ; - sh:closed true ; - sh:description "an item that refers to a collection of data from a data source." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Dataset . + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Transcript . -biolink:DatasetDistribution a sh:NodeShape ; +biolink:ChemicalMixture a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalEntity ; sh:closed true ; - sh:description "an item that holds distribution level information about a dataset." ; + sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:distribution_download_url ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:creation_date ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:order 12 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:full_name ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:rights ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 19 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:format ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:license ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:DatasetDistribution . - -biolink:Device a sh:NodeShape ; - sh:closed true ; - sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:order 1 ; - sh:path biolink:xref ], + sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + sh:description "" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:Device . + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ] ; + sh:targetClass biolink:ChemicalMixture . -biolink:Exon a sh:NodeShape ; +biolink:ClinicalAttribute a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; + sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:path biolink:full_name ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ] ; - sh:targetClass biolink:Exon . - -biolink:GeneFamily a sh:NodeShape ; - sh:closed true ; - sh:description "any grouping of multiple genes or gene products related by common descent" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:iri ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:category ], + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:datatype xsd:string ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:GeneFamily . - -biolink:GeneProductMixin a sh:NodeShape ; - sh:closed false ; - sh:description "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GeneProductMixin . + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ] ; + sh:targetClass biolink:ClinicalAttribute . -biolink:GeneticInheritance a sh:NodeShape ; +biolink:FunctionalAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:Association ; sh:closed true ; - sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; + sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:GeneticInheritance . - -biolink:InformationContentEntity a sh:NodeShape ; - sh:closed false ; - sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; sh:order 12 ; - sh:path rdfs:label ], + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:id ], + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:InformationContentEntity . - -biolink:Onset a sh:NodeShape ; - sh:closed true ; - sh:description "The age group in which (disease) symptom manifestations appear." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; sh:order 11 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:Onset . + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ] ; + sh:targetClass biolink:FunctionalAssociation . -biolink:OrganismalEntity a sh:NodeShape ; - sh:closed false ; - sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; +biolink:LifeStage a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismalEntity ; + sh:closed true ; + sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:OrganismalEntity . + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ] ; + sh:targetClass biolink:LifeStage . -biolink:PredicateMapping a sh:NodeShape ; +biolink:NucleicAcidEntity a sh:NodeShape ; + rdfs:subClassOf biolink:MolecularEntity ; sh:closed true ; - sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; + sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:path biolink:xref ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], + sh:order 9 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 7 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:exact_match ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:object_part_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:subject_part_qualifier ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], + sh:path biolink:is_metabolite ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; - sh:path biolink:narrow_match ], + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:object_context_qualifier ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:causal_mechanism_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:qualified_predicate ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:object_derivative_qualifier ] ; - sh:targetClass biolink:PredicateMapping . + sh:path biolink:synonym ] ; + sh:targetClass biolink:NucleicAcidEntity . -biolink:Procedure a sh:NodeShape ; +biolink:CellularOrganism a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismalEntity ; sh:closed true ; - sh:description "A series of actions conducted in a certain order or manner" ; + sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:Procedure . + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:CellularOrganism . -biolink:SocioeconomicAttribute a sh:NodeShape ; +biolink:GeneToDiseaseAssociation a sh:NodeShape ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; sh:closed true ; - sh:description "Attributes relating to a socioeconomic manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:path biolink:sex_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; - sh:targetClass biolink:SocioeconomicAttribute . - -biolink:TaxonomicRank a sh:NodeShape ; - sh:closed true ; - sh:description "A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ] ; - sh:targetClass biolink:TaxonomicRank . - -biolink:Treatment a sh:NodeShape ; - sh:closed true ; - sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; sh:order 9 ; - sh:path biolink:iri ], + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Device ; - sh:description "connects an entity to one or more (medical) devices" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_device ], - [ sh:class biolink:Drug ; - sh:description "connects an entity to one or more drugs" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_drug ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 3 ; - sh:path biolink:timepoint ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Procedure ; - sh:description "connects an entity to one or more (medical) procedures" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_procedure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Treatment . - -biolink:Zygosity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:Zygosity . - -biolink:Case a sh:NodeShape ; - sh:closed true ; - sh:description "An individual (human) organism that has a patient role in some clinical context." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:Case . + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . -biolink:CellLine a sh:NodeShape ; +biolink:MolecularActivity a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; sh:closed true ; + sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 0 ; + sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the output for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; sh:path biolink:iri ], + [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the input for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:CellLine . + sh:path biolink:full_name ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "The gene product, gene, or complex that catalyzes the reaction" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ] ; + sh:targetClass biolink:MolecularActivity . -biolink:IndividualOrganism a sh:NodeShape ; +biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismalEntity ; sh:closed true ; - sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; + sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:IndividualOrganism . + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:PopulationOfIndividualOrganisms . -biolink:Outcome a sh:NodeShape ; +biolink:StudyResult a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; sh:closed false ; - sh:description "An entity that has the role of being the consequence of an exposure event. This is an abstract mixin grouping of various categories of possible biological or non-biological (e.g. clinical) outcomes." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:Outcome . - -biolink:Transcript a sh:NodeShape ; - sh:closed true ; - sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; + sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Transcript . - -biolink:BiologicalProcess a sh:NodeShape ; - sh:closed true ; - sh:description "One or more causally connected executions of molecular functions" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:has_output ], + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:BiologicalProcess . + sh:path biolink:full_name ] ; + sh:targetClass biolink:StudyResult . -biolink:Drug a sh:NodeShape ; +biolink:BiologicalProcess a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; sh:closed true ; - sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; + sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 4 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:trade_name ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; sh:order 1 ; - sh:path biolink:is_supplement ], + sh:path biolink:has_input ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 19 ; + sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:iri ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:drug_regulatory_status_world_wide ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; + sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:available_from ], + sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:Drug . + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ] ; + sh:targetClass biolink:BiologicalProcess . -biolink:ExposureEvent a sh:NodeShape ; +biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; sh:closed false ; - sh:description "A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes" ; + sh:description "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a point in time" ; + sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProduct . + +biolink:MacromolecularMachineMixin a sh:NodeShape ; + sh:closed false ; + sh:description "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:id ] ; - sh:targetClass biolink:ExposureEvent . + sh:path rdfs:label ] ; + sh:targetClass biolink:MacromolecularMachineMixin . -biolink:MaterialSample a sh:NodeShape ; +biolink:PhysicalEntity a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; sh:closed true ; - sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; + sh:description "An entity that has material reality (a.k.a. physical essence)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:PhysicalEntity . + +biolink:Genotype a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 2 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], + [ sh:class biolink:Zygosity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 11 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ] ; - sh:targetClass biolink:MaterialSample . + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:id ] ; + sh:targetClass biolink:Genotype . -biolink:Pathway a sh:NodeShape ; +biolink:MolecularEntity a sh:NodeShape ; + rdfs:subClassOf biolink:ChemicalEntity ; sh:closed true ; + sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_metabolite ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_input ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 16 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 15 ; + sh:order 16 ; sh:path biolink:has_attribute ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:id ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ] ; + sh:targetClass biolink:MolecularEntity . + +biolink:OrganismalEntity a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed false ; + sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ] ; - sh:targetClass biolink:Pathway . - -biolink:LifeStage a sh:NodeShape ; - sh:closed true ; - sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:LifeStage . + sh:path rdfs:label ] ; + sh:targetClass biolink:OrganismalEntity . -biolink:NucleicAcidEntity a sh:NodeShape ; +biolink:SequenceVariant a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; + sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_metabolite ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 11 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:trade_name ], + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 20 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 10 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:order 16 ; - sh:path rdf:type ] ; - sh:targetClass biolink:NucleicAcidEntity . - -biolink:MolecularActivity a sh:NodeShape ; - sh:closed true ; - sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "The gene product, gene, or complex that catalyzes the reaction" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the input for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the output for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], + sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:MolecularActivity . + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:SequenceVariant . -biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; +biolink:Agent a sh:NodeShape ; + rdfs:subClassOf biolink:AdministrativeEntity ; sh:closed true ; - sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; + sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:address ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:affiliation ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ] ; - sh:targetClass biolink:PopulationOfIndividualOrganisms . - -biolink:MacromolecularMachineMixin a sh:NodeShape ; - sh:closed false ; - sh:description "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:MacromolecularMachineMixin . + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:Agent . -biolink:MolecularEntity a sh:NodeShape ; +biolink:ChemicalRole a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; + sh:description "A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:is_metabolite ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path rdfs:label ], + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; sh:order 1 ; - sh:path biolink:trade_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 16 ; + sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path dct:description ] ; - sh:targetClass biolink:MolecularEntity . - -biolink:PhysicalEntity a sh:NodeShape ; - sh:closed true ; - sh:description "An entity that has material reality (a.k.a. physical essence)." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; sh:path biolink:category ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:id ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path rdf:type ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; sh:path rdfs:label ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:PhysicalEntity . + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ] ; + sh:targetClass biolink:ChemicalRole . -biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; +biolink:InformationContentEntity a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; sh:closed false ; - sh:description "A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProduct . - -biolink:Genotype a sh:NodeShape ; - sh:closed true ; - sh:description "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; + sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Zygosity ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 6 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 7 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:Genotype . - -biolink:SequenceVariant a sh:NodeShape ; - sh:closed true ; - sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 2 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ] ; + sh:targetClass biolink:InformationContentEntity . + +biolink:PhenotypicFeature a sh:NodeShape ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; + sh:closed true ; + sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 3 ; + sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:provided_by ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "The state of the sequence w.r.t a reference sequence" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ] ; - sh:targetClass biolink:SequenceVariant . + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ] ; + sh:targetClass biolink:PhenotypicFeature . biolink:ChemicalEntity a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:category ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 9 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:ChemicalEntity . + +biolink:Gene a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; + sh:closed true ; + sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Symbol for a particular thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:symbol ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; - sh:path biolink:has_chemical_role ], + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 5 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:provided_by ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ] ; - sh:targetClass biolink:ChemicalEntity . + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ] ; + sh:targetClass biolink:Gene . -biolink:Agent a sh:NodeShape ; +biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; + rdfs:subClassOf biolink:BiologicalEntity ; sh:closed true ; - sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; + sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:address ], - [ sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; - sh:order 0 ; - sh:path biolink:affiliation ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ] ; - sh:targetClass biolink:Agent . + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeature . -biolink:PhenotypicFeature a sh:NodeShape ; +biolink:Disease a sh:NodeShape ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; sh:closed true ; - sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; + sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "a human-readable description of an entity" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], [ sh:class biolink:Attribute ; @@ -30814,36 +37070,52 @@ biolink:PhenotypicFeature a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:PhenotypicFeature . + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:Disease . -biolink:ChemicalRole a sh:NodeShape ; +biolink:BiologicalSex a sh:NodeShape ; + rdfs:subClassOf biolink:Attribute ; sh:closed true ; - sh:description "A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -30851,31 +37123,15 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], [ sh:class biolink:Attribute ; @@ -30888,35 +37144,101 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:BiologicalSex . + +biolink:BiologicalEntity a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:ChemicalRole . - -biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; - sh:closed true ; - sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A human-readable name for an attribute or entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -30925,818 +37247,975 @@ biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a long-form human readable name for a thing" ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:BiologicalEntity . + +biolink:AnatomicalEntity a sh:NodeShape ; + rdfs:subClassOf biolink:OrganismalEntity ; + sh:closed true ; + sh:description "A subcellular location, cell type or gross anatomical part" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeature . + sh:targetClass biolink:AnatomicalEntity . -biolink:Gene a sh:NodeShape ; +biolink:GeneOrGeneProduct a sh:NodeShape ; + rdfs:subClassOf biolink:MacromolecularMachineMixin ; + sh:closed false ; + sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:GeneOrGeneProduct . + +biolink:QuantityValue a sh:NodeShape ; + rdfs:subClassOf biolink:Annotation ; sh:closed true ; - sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; + sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:double ; + sh:description "connects a quantity value to a number" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Symbol for a particular thing" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_numeric_value ], + [ sh:datatype ; + sh:description "connects a quantity value to a unit" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:symbol ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:description "connects a genomic feature to its sequence" ; + sh:path biolink:has_unit ] ; + sh:targetClass biolink:QuantityValue . + +biolink:Association a sh:NodeShape ; + rdfs:subClassOf biolink:Entity ; + sh:closed true ; + sh:description "A typed association between two entities, supported by evidence" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 3 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 15 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ] ; - sh:targetClass biolink:Gene . - -biolink:Disease a sh:NodeShape ; - sh:closed true ; - sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 12 ; + sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:iri ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; - sh:targetClass biolink:Disease . + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ] ; + sh:targetClass biolink:Association . -biolink:BiologicalSex a sh:NodeShape ; +biolink:OrganismTaxon a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; sh:closed true ; + sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 10 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:category ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:TaxonomicRank ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 0 ; + sh:path biolink:has_taxonomic_rank ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 14 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path biolink:deprecated ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:full_name ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ] ; - sh:targetClass biolink:BiologicalSex . + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:provided_by ] ; + sh:targetClass biolink:OrganismTaxon . -biolink:AnatomicalEntity a sh:NodeShape ; +biolink:EvidenceType a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; sh:closed true ; - sh:description "A subcellular location, cell type or gross anatomical part" ; + sh:description "Class of evidence that supports an association" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ], + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:description "The human readable scientific name for the taxon of the entity." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; + sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:has_attribute ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 11 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:AnatomicalEntity . - -biolink:GeneOrGeneProduct a sh:NodeShape ; - sh:closed false ; - sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:GeneOrGeneProduct . - -biolink:QuantityValue a sh:NodeShape ; - sh:closed true ; - sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:description "connects a quantity value to a number" ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_numeric_value ], - [ sh:description "connects a quantity value to a unit" ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:has_unit ] ; - sh:targetClass biolink:QuantityValue . + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:EvidenceType . -biolink:OrganismTaxon a sh:NodeShape ; +biolink:RetrievalSource a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; sh:closed true ; - sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; + sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 4 ; - sh:path biolink:synonym ], + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:path biolink:synonym ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path biolink:iri ], - [ sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:full_name ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 2 ; - sh:path biolink:xref ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 11 ; + sh:order 17 ; sh:path biolink:has_attribute ], - [ sh:class biolink:TaxonomicRank ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_taxonomic_rank ], - [ sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 7 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:deprecated ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:order 8 ; - sh:path rdf:type ] ; - sh:targetClass biolink:OrganismTaxon . - -biolink:NamedThing a sh:NodeShape ; - sh:closed true ; - sh:description "a databased entity or concept/class" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:path biolink:resource_id ], + [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:minCount 1 ; sh:order 1 ; - sh:path biolink:xref ], + sh:path biolink:resource_role ], [ sh:datatype xsd:string ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:upstream_resource_ids ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:NamedThing . + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:RetrievalSource . -biolink:EvidenceType a sh:NodeShape ; +biolink:Study a sh:NodeShape ; + rdfs:subClassOf biolink:Activity ; sh:closed true ; - sh:description "Class of evidence that supports an association" ; + sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:xref ], + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 14 ; + sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 6 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 7 ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:format ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; sh:path biolink:id ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:creation_date ] ; - sh:targetClass biolink:EvidenceType . + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ] ; + sh:targetClass biolink:Study . biolink:Publication a sh:NodeShape ; + rdfs:subClassOf biolink:InformationContentEntity ; sh:closed true ; sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:order 1 ; - sh:path biolink:pages ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:summary ], - [ sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:order 3 ; - sh:path biolink:keywords ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 18 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:order 17 ; - sh:path rdf:type ], + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:order 6 ; - sh:path dct:type ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:description "mesh terms tagging a publication" ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:mesh_terms ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:format ] ; - sh:targetClass biolink:Publication . - -biolink:RetrievalSource a sh:NodeShape ; - sh:closed true ; - sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; - sh:order 13 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; sh:path biolink:category ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:creation_date ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:order 16 ; - sh:path dct:description ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 8 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:order 9 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; sh:path biolink:full_name ], - [ sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:upstream_resource_ids ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:format ], - [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:resource_role ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; - sh:order 4 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; sh:path biolink:license ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 18 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; sh:path biolink:deprecated ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:iri ], - [ sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:resource_id ], - [ sh:datatype xsd:string ; - sh:order 14 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:rights ], - [ sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:summary ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; - sh:order 15 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:RetrievalSource . + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ] ; + sh:targetClass biolink:Publication . -biolink:Study a sh:NodeShape ; +biolink:NamedThing a sh:NodeShape ; + rdfs:subClassOf biolink:Entity ; sh:closed true ; - sh:description "a detailed investigation and/or analysis" ; + sh:description "a databased entity or concept/class" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 6 ; - sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], - [ sh:description "Alternate human-readable names for a thing" ; - sh:order 3 ; - sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Study . + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ] ; + sh:targetClass biolink:NamedThing . biolink:Attribute a sh:NodeShape ; + rdfs:subClassOf biolink:NamedThing ; sh:closed true ; sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Alternate human-readable names for a thing" ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path dct:description ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -31744,16 +38223,35 @@ biolink:Attribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; @@ -31764,6 +38262,7 @@ biolink:OntologyClass a sh:NodeShape ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ] ; sh:targetClass biolink:OntologyClass . diff --git a/project/shex/biolink_model.shex b/project/shex/biolink_model.shex index 7d11ef096..acaa3bc6b 100644 --- a/project/shex/biolink_model.shex +++ b/project/shex/biolink_model.shex @@ -1,3 +1,5 @@ +# metamodel_version: 1.7.0 +# version: 4.2.4 BASE PREFIX rdf: PREFIX rdfs: @@ -4329,4 +4331,3 @@ linkml:Sparqlpath xsd:string ) } - diff --git a/src/biolink_model/datamodel/model.py b/src/biolink_model/datamodel/model.py index b0a40f1f4..ba1772a86 100644 --- a/src/biolink_model/datamodel/model.py +++ b/src/biolink_model/datamodel/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-10-10T17:39:00 +# Generation date: 2024-10-10T16:30:08 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -11,7 +11,7 @@ from jsonasobj2 import JsonObj, as_dict from typing import Optional, List, Union, Dict, ClassVar, Any from dataclasses import dataclass -from datetime import date, datetime +from datetime import date, datetime, time from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions from linkml_runtime.utils.slot import Slot @@ -1383,7 +1383,7 @@ class OrganismTaxonToEnvironmentAssociationId(AssociationId): pass -@dataclass +@dataclass(repr=False) class MappingCollection(YAMLRoot): """ A collection of deprecated mappings. @@ -1405,7 +1405,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class PredicateMapping(YAMLRoot): """ A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should @@ -1512,7 +1512,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class OntologyClass(YAMLRoot): """ a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be @@ -1550,7 +1550,7 @@ class Annotation(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.Annotation -@dataclass +@dataclass(repr=False) class QuantityValue(Annotation): """ A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric @@ -1616,7 +1616,7 @@ class PathognomonicityQuantifier(SpecificityQuantifier): class_model_uri: ClassVar[URIRef] = BIOLINK.PathognomonicityQuantifier -@dataclass +@dataclass(repr=False) class FrequencyQuantifier(RelationshipQuantifier): _inherited_slots: ClassVar[List[str]] = [] @@ -1655,7 +1655,7 @@ class ChemicalOrDrugOrTreatment(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalOrDrugOrTreatment -@dataclass +@dataclass(repr=False) class Entity(YAMLRoot): """ Root Biolink Model class for all things and informational relationships, real or imagined. @@ -1734,7 +1734,7 @@ def __new__(cls, *args, **kwargs): -@dataclass +@dataclass(repr=False) class NamedThing(Entity): """ a databased entity or concept/class @@ -1813,7 +1813,7 @@ def __new__(cls, *args, **kwargs): -@dataclass +@dataclass(repr=False) class Attribute(NamedThing): """ A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, @@ -1866,7 +1866,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalRole(Attribute): """ A role played by the molecular entity or part thereof within a chemical context. @@ -1896,7 +1896,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BiologicalSex(Attribute): _inherited_slots: ClassVar[List[str]] = [] @@ -1923,7 +1923,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhenotypicSex(BiologicalSex): """ An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present. @@ -1953,7 +1953,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypicSex(BiologicalSex): """ An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex @@ -1984,7 +1984,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SeverityValue(Attribute): """ describes the severity of a phenotypic feature or disease @@ -2014,7 +2014,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RelationshipType(OntologyClass): """ An OWL property used as an edge label @@ -2037,7 +2037,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class TaxonomicRank(OntologyClass): """ A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom) @@ -2060,7 +2060,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class OrganismTaxon(NamedThing): """ A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). @@ -2094,7 +2094,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Event(NamedThing): """ Something that happens at a given place and time. @@ -2123,7 +2123,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AdministrativeEntity(NamedThing): _inherited_slots: ClassVar[List[str]] = [] @@ -2145,7 +2145,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Agent(AdministrativeEntity): """ person, group, organization or project that provides a piece of information (i.e. a knowledge association) @@ -2187,7 +2187,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class InformationContentEntity(NamedThing): """ a piece of information that typically describes some topic of discourse or is used as support. @@ -2227,7 +2227,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class StudyResult(InformationContentEntity): """ A collection of data items from a study that are about a particular study subject or experimental unit (the @@ -2254,7 +2254,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class StudyVariable(InformationContentEntity): """ a variable that is used as a measure in the investigation of a study @@ -2283,7 +2283,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CommonDataElement(InformationContentEntity): """ A Common Data Element (CDE) is a standardized, precisely defined question, paired with a set of allowable @@ -2314,7 +2314,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ConceptCountAnalysisResult(StudyResult): """ A result of a concept count analysis. @@ -2343,7 +2343,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ObservedExpectedFrequencyAnalysisResult(StudyResult): """ A result of a observed expected frequency analysis. @@ -2372,7 +2372,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RelativeFrequencyAnalysisResult(StudyResult): """ A result of a relative frequency analysis. @@ -2401,7 +2401,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class TextMiningResult(StudyResult): """ A result of text mining. @@ -2430,7 +2430,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChiSquaredAnalysisResult(StudyResult): """ A result of a chi squared analysis. @@ -2459,7 +2459,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class LogOddsAnalysisResult(StudyResult): """ A result of a log odds ratio analysis. @@ -2488,7 +2488,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Dataset(InformationContentEntity): """ an item that refers to a collection of data from a data source. @@ -2517,7 +2517,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DatasetDistribution(InformationContentEntity): """ an item that holds distribution level information about a dataset. @@ -2550,7 +2550,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DatasetVersion(InformationContentEntity): """ an item that holds version level information about a dataset. @@ -2591,7 +2591,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DatasetSummary(InformationContentEntity): """ an item that holds summary level information about a dataset. @@ -2628,7 +2628,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ConfidenceLevel(InformationContentEntity): """ Level of confidence in a statement @@ -2657,7 +2657,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EvidenceType(InformationContentEntity): """ Class of evidence that supports an association @@ -2686,7 +2686,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Publication(InformationContentEntity): """ Any ‘published’ piece of information. Publications are considered broadly to include any document or document part @@ -2759,7 +2759,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Book(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -2794,7 +2794,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BookChapter(Publication): _inherited_slots: ClassVar[List[str]] = [] @@ -2835,7 +2835,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Serial(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. @@ -2882,7 +2882,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Article(Publication): """ a piece of writing on a particular topic presented as a stand-alone section of a larger publication @@ -2930,7 +2930,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class JournalArticle(Article): """ an article, typically presenting results of research, that is published in an issue of a scientific journal. @@ -2961,7 +2961,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Patent(Publication): """ a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use @@ -2992,7 +2992,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class WebPage(Publication): """ a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, @@ -3023,7 +3023,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PreprintPublication(Publication): """ a document reresenting an early version of an author's original scholarly work, such as a research paper or a @@ -3054,7 +3054,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DrugLabel(Publication): """ a document accompanying a drug or its container that provides written, printed or graphic information about the @@ -3086,7 +3086,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RetrievalSource(InformationContentEntity): """ Provides information about how a particular InformationResource served as a source from which knowledge expressed @@ -3161,7 +3161,7 @@ class PhysicalEssence(PhysicalEssenceOrOccurrent): class_model_uri: ClassVar[URIRef] = BIOLINK.PhysicalEssence -@dataclass +@dataclass(repr=False) class PhysicalEntity(NamedThing): """ An entity that has material reality (a.k.a. physical essence). @@ -3214,7 +3214,7 @@ class ActivityAndBehavior(Occurrent): class_model_uri: ClassVar[URIRef] = BIOLINK.ActivityAndBehavior -@dataclass +@dataclass(repr=False) class Activity(NamedThing): """ An activity is something that occurs over a period of time and acts upon or with entities; it may include @@ -3244,7 +3244,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Study(Activity): """ a detailed investigation and/or analysis @@ -3273,7 +3273,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Procedure(NamedThing): """ A series of actions conducted in a certain order or manner @@ -3302,7 +3302,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Phenomenon(NamedThing): """ a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question @@ -3331,7 +3331,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Device(NamedThing): """ A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment @@ -3360,7 +3360,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiagnosticAid(NamedThing): """ A device or substance used to help diagnose disease or injury @@ -3401,7 +3401,7 @@ class SubjectOfInvestigation(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.SubjectOfInvestigation -@dataclass +@dataclass(repr=False) class MaterialSample(PhysicalEntity): """ A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a @@ -3432,7 +3432,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PlanetaryEntity(NamedThing): """ Any entity or process that exists at the level of the whole planet @@ -3461,7 +3461,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EnvironmentalProcess(PlanetaryEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -3487,7 +3487,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EnvironmentalFeature(PlanetaryEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -3513,7 +3513,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeographicLocation(PlanetaryEntity): """ a location that can be described in lat/long coordinates @@ -3550,7 +3550,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeographicLocationAtTime(GeographicLocation): """ a location that can be described in lat/long coordinates, for a particular time @@ -3583,7 +3583,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ThingWithTaxon(YAMLRoot): """ A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; @@ -3610,7 +3610,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class BiologicalEntity(NamedThing): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -3640,7 +3640,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenomicEntity(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -3658,7 +3658,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class EpigenomicEntity(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -3676,7 +3676,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class ChemicalEntity(NamedThing): """ A chemical entity is a physical entity that pertains to chemistry or biochemistry. @@ -3727,7 +3727,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularEntity(ChemicalEntity): """ A molecular entity is a chemical entity composed of individual or covalently bonded atoms. @@ -3760,7 +3760,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SmallMolecule(MolecularEntity): """ A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, @@ -3792,7 +3792,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalMixture(ChemicalEntity): """ A chemical mixture is a chemical entity composed of two or more molecular entities. @@ -3838,7 +3838,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NucleicAcidEntity(MolecularEntity): """ A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based @@ -3882,7 +3882,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RegulatoryRegion(BiologicalEntity): """ A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- @@ -3916,7 +3916,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AccessibleDnaRegion(RegulatoryRegion): """ A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as @@ -3950,7 +3950,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class TranscriptionFactorBindingSite(RegulatoryRegion): """ A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that @@ -3984,7 +3984,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularMixture(ChemicalMixture): """ A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and @@ -4014,7 +4014,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ComplexMolecularMixture(ChemicalMixture): """ A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown @@ -4044,7 +4044,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BiologicalProcessOrActivity(BiologicalEntity): """ Either an individual molecular activity, or a collection of causally connected molecular activities in a @@ -4089,7 +4089,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularActivity(BiologicalProcessOrActivity): """ An execution of a molecular function carried out by a gene product or macromolecular complex. @@ -4133,7 +4133,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BiologicalProcess(BiologicalProcessOrActivity): """ One or more causally connected executions of molecular functions @@ -4162,7 +4162,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Pathway(BiologicalProcess): _inherited_slots: ClassVar[List[str]] = ["in_taxon", "has_input", "has_output", "enabled_by"] @@ -4188,7 +4188,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhysiologicalProcess(BiologicalProcess): _inherited_slots: ClassVar[List[str]] = ["in_taxon", "has_input", "has_output", "enabled_by"] @@ -4214,7 +4214,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Behavior(BiologicalProcess): _inherited_slots: ClassVar[List[str]] = ["in_taxon", "has_input", "has_output", "enabled_by"] @@ -4240,7 +4240,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProcessedMaterial(ChemicalMixture): """ A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a @@ -4270,7 +4270,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Drug(MolecularMixture): """ A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease @@ -4299,7 +4299,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EnvironmentalFoodContaminant(ChemicalEntity): _inherited_slots: ClassVar[List[str]] = ["has_chemical_role"] @@ -4325,7 +4325,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class FoodAdditive(ChemicalEntity): _inherited_slots: ClassVar[List[str]] = ["has_chemical_role"] @@ -4351,7 +4351,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Food(ChemicalMixture): """ A substance consumed by a living organism as a source of nutrition @@ -4380,7 +4380,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismAttribute(Attribute): """ describes a characteristic of an organismal entity. @@ -4410,7 +4410,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhenotypicQuality(OrganismAttribute): """ A property of a phenotype @@ -4440,7 +4440,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneticInheritance(BiologicalEntity): """ The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, @@ -4470,7 +4470,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismalEntity(BiologicalEntity): """ A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding @@ -4500,7 +4500,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Bacterium(OrganismalEntity): """ A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and @@ -4530,7 +4530,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Virus(OrganismalEntity): """ A virus is a microorganism that replicates itself as a microRNA and infects the host cell. @@ -4559,7 +4559,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellularOrganism(OrganismalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -4585,7 +4585,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Mammal(CellularOrganism): """ A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the @@ -4615,7 +4615,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Human(Mammal): """ A member of the the species Homo sapiens. @@ -4644,7 +4644,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Plant(CellularOrganism): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -4670,7 +4670,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Invertebrate(CellularOrganism): """ An animal lacking a vertebral column. This group consists of 98% of all animal species. @@ -4699,7 +4699,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Vertebrate(CellularOrganism): """ A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column. @@ -4728,7 +4728,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Fungus(CellularOrganism): """ A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, @@ -4759,7 +4759,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class LifeStage(OrganismalEntity): """ A stage of development or growth of an organism, including post-natal adult stages @@ -4788,7 +4788,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class IndividualOrganism(OrganismalEntity): """ An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: @@ -4818,7 +4818,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PopulationOfIndividualOrganisms(OrganismalEntity): """ A collection of individuals from the same taxonomic class distinguished by one or more characteristics. @@ -4848,7 +4848,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class StudyPopulation(PopulationOfIndividualOrganisms): """ A group of people banded together or treated as a group as participants in a research study. @@ -4877,7 +4877,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeature(BiologicalEntity): """ Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these @@ -4909,7 +4909,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Disease(DiseaseOrPhenotypicFeature): """ A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that @@ -4940,7 +4940,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhenotypicFeature(DiseaseOrPhenotypicFeature): """ A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an @@ -4970,7 +4970,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BehavioralFeature(PhenotypicFeature): """ A phenotypic feature which is behavioral in nature. @@ -4999,7 +4999,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AnatomicalEntity(OrganismalEntity): """ A subcellular location, cell type or gross anatomical part @@ -5028,7 +5028,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellularComponent(AnatomicalEntity): """ A location in or around a cell @@ -5057,7 +5057,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Cell(AnatomicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5083,7 +5083,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellLine(OrganismalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5109,7 +5109,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GrossAnatomicalStructure(AnatomicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5161,7 +5161,7 @@ class ChemicalEntityOrProteinOrPolypeptide(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalEntityOrProteinOrPolypeptide -@dataclass +@dataclass(repr=False) class MacromolecularMachineMixin(YAMLRoot): """ A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. @@ -5195,7 +5195,7 @@ class GeneOrGeneProduct(MacromolecularMachineMixin): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneOrGeneProduct -@dataclass +@dataclass(repr=False) class Gene(BiologicalEntity): """ A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A @@ -5242,7 +5242,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneProductMixin(GeneOrGeneProduct): """ The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA @@ -5284,7 +5284,7 @@ class GeneProductIsoformMixin(GeneProductMixin): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneProductIsoformMixin -@dataclass +@dataclass(repr=False) class MacromolecularComplex(BiologicalEntity): """ A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which @@ -5318,7 +5318,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NucleosomeModification(BiologicalEntity): """ A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a @@ -5366,7 +5366,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Genome(BiologicalEntity): """ A genome is the sum of genetic material within a cell or virion. @@ -5399,7 +5399,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Exon(BiologicalEntity): """ A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA @@ -5429,7 +5429,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Transcript(BiologicalEntity): """ An RNA synthesized on a DNA or RNA template by an RNA polymerase. @@ -5458,7 +5458,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CodingSequence(BiologicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5488,7 +5488,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Polypeptide(BiologicalEntity): """ A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based @@ -5519,7 +5519,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Protein(Polypeptide): """ A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated @@ -5563,7 +5563,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProteinIsoform(Protein): """ Represents a protein that is a specific isoform of the canonical or reference protein. See @@ -5607,7 +5607,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProteinDomain(BiologicalEntity): """ A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently @@ -5643,7 +5643,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PosttranslationalModification(BiologicalEntity): """ A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to @@ -5687,7 +5687,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProteinFamily(BiologicalEntity): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5718,7 +5718,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NucleicAcidSequenceMotif(BiologicalEntity): """ A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological @@ -5748,7 +5748,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RNAProduct(Transcript): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5788,7 +5788,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class RNAProductIsoform(RNAProduct): """ Represents a protein that is a specific isoform of the canonical or reference RNA @@ -5831,7 +5831,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NoncodingRNAProduct(RNAProduct): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5857,7 +5857,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MicroRNA(NoncodingRNAProduct): _inherited_slots: ClassVar[List[str]] = ["in_taxon"] @@ -5883,7 +5883,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SiRNA(NoncodingRNAProduct): """ A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular @@ -5914,7 +5914,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneGroupingMixin(YAMLRoot): """ any grouping of multiple genes or gene products @@ -5936,7 +5936,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GeneFamily(BiologicalEntity): """ any grouping of multiple genes or gene products related by common descent @@ -5970,7 +5970,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Zygosity(Attribute): _inherited_slots: ClassVar[List[str]] = [] @@ -5997,7 +5997,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Genotype(BiologicalEntity): """ An information content entity that describes a genome by specifying the total variation in genomic sequence and/or @@ -6035,7 +6035,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Haplotype(BiologicalEntity): """ A set of zero or more Alleles on a single instance of a Sequence[VMC] @@ -6068,7 +6068,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SequenceVariant(BiologicalEntity): """ A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. @@ -6106,7 +6106,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Snv(SequenceVariant): """ SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist @@ -6135,7 +6135,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ReagentTargetedGene(BiologicalEntity): """ A gene altered in its expression level in the context of some experiment as a result of being targeted by @@ -6169,7 +6169,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalAttribute(Attribute): """ Attributes relating to a clinical manifestation @@ -6199,7 +6199,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalMeasurement(ClinicalAttribute): """ A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject @@ -6235,7 +6235,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalModifier(ClinicalAttribute): """ Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, @@ -6266,7 +6266,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalCourse(ClinicalAttribute): """ The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the @@ -6297,7 +6297,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Onset(ClinicalCourse): """ The age group in which (disease) symptom manifestations appear. @@ -6327,7 +6327,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalEntity(NamedThing): """ Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed @@ -6357,7 +6357,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalTrial(ClinicalEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -6383,7 +6383,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalIntervention(ClinicalEntity): _inherited_slots: ClassVar[List[str]] = [] @@ -6409,7 +6409,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ClinicalFinding(PhenotypicFeature): """ this category is currently considered broad enough to tag clinical lab measurements and other biological @@ -6444,7 +6444,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Hospitalization(ClinicalIntervention): _inherited_slots: ClassVar[List[str]] = [] @@ -6470,7 +6470,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SocioeconomicAttribute(Attribute): """ Attributes relating to a socioeconomic manifestation @@ -6500,7 +6500,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Case(IndividualOrganism): """ An individual (human) organism that has a patient role in some clinical context. @@ -6529,7 +6529,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Cohort(StudyPopulation): """ A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a @@ -6559,7 +6559,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ExposureEvent(OntologyClass): """ A (possibly time bounded) incidence of a feature of the environment of an organism that influences one or more @@ -6582,7 +6582,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GenomicBackgroundExposure(Attribute): """ A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or @@ -6648,7 +6648,7 @@ class PathologicalEntityMixin(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.PathologicalEntityMixin -@dataclass +@dataclass(repr=False) class PathologicalProcess(BiologicalProcess): """ A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, @@ -6678,7 +6678,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PathologicalProcessExposure(Attribute): """ A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an @@ -6713,7 +6713,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PathologicalAnatomicalStructure(AnatomicalEntity): """ An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, @@ -6743,7 +6743,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PathologicalAnatomicalExposure(Attribute): """ An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or @@ -6778,7 +6778,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeatureExposure(Attribute): """ A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or @@ -6814,7 +6814,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalExposure(Attribute): """ A chemical exposure is an intake of a particular chemical entity. @@ -6853,7 +6853,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ComplexChemicalExposure(Attribute): """ A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug. @@ -6883,7 +6883,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DrugExposure(ChemicalExposure): """ A drug exposure is an intake of a particular drug. @@ -6917,7 +6917,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DrugToGeneInteractionExposure(DrugExposure): """ drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are @@ -6953,7 +6953,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class Treatment(NamedThing): """ A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices @@ -7002,7 +7002,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BioticExposure(Attribute): """ An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses). @@ -7036,7 +7036,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EnvironmentalExposure(Attribute): """ A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), @@ -7071,7 +7071,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeographicExposure(EnvironmentalExposure): """ A geographic exposure is a factor relating to geographic proximity to some impactful entity. @@ -7105,7 +7105,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BehavioralExposure(Attribute): """ A behavioral exposure is a factor relating to behavior impacting an individual. @@ -7139,7 +7139,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SocioeconomicExposure(Attribute): """ A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. @@ -7293,7 +7293,7 @@ class SocioeconomicOutcome(YAMLRoot): class_model_uri: ClassVar[URIRef] = BIOLINK.SocioeconomicOutcome -@dataclass +@dataclass(repr=False) class Association(Entity): """ A typed association between two entities, supported by evidence @@ -7309,8 +7309,8 @@ class Association(Entity): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None negated: Optional[Union[bool, Bool]] = None qualifier: Optional[str] = None qualifiers: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() @@ -7500,7 +7500,7 @@ def __new__(cls, *args, **kwargs): -@dataclass +@dataclass(repr=False) class ChemicalEntityAssessesNamedThingAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -7510,11 +7510,11 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalEntityAssessesNamedThingAssociation id: Union[str, ChemicalEntityAssessesNamedThingAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7543,7 +7543,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ContributorAssociation(Association): """ Any association between an entity (such as a publication) and various agents that contribute to its realisation @@ -7556,11 +7556,11 @@ class ContributorAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ContributorAssociation id: Union[str, ContributorAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, InformationContentEntityId] = None predicate: Union[str, PredicateType] = None object: Union[str, AgentId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" qualifiers: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -7594,7 +7594,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeToGenotypePartAssociation(Association): """ Any association between one genotype and a genotypic entity that is a sub-component of it @@ -7607,11 +7607,11 @@ class GenotypeToGenotypePartAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeToGenotypePartAssociation id: Union[str, GenotypeToGenotypePartAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None object: Union[str, GenotypeId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7640,7 +7640,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeToGeneAssociation(Association): """ Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single @@ -7654,11 +7654,11 @@ class GenotypeToGeneAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeToGeneAssociation id: Union[str, GenotypeToGeneAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None object: Union[str, GeneId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7687,7 +7687,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeToVariantAssociation(Association): """ Any association between a genotype and a sequence variant. @@ -7700,11 +7700,11 @@ class GenotypeToVariantAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeToVariantAssociation id: Union[str, GenotypeToVariantAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None object: Union[str, SequenceVariantId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7733,7 +7733,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGeneAssociation(Association): """ abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes @@ -7748,10 +7748,10 @@ class GeneToGeneAssociation(Association): id: Union[str, GeneToGeneAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): @@ -7770,7 +7770,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGeneHomologyAssociation(GeneToGeneAssociation): """ A homology association between two genes. May be orthology (in which case the species of subject and object should @@ -7784,11 +7784,11 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToGeneHomologyAssociation id: Union[str, GeneToGeneHomologyAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7817,7 +7817,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGeneFamilyAssociation(Association): """ Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence @@ -7832,11 +7832,11 @@ class GeneToGeneFamilyAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToGeneFamilyAssociation id: Union[str, GeneToGeneFamilyAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, GeneId] = None object: Union[str, GeneFamilyId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7865,7 +7865,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneExpressionMixin(YAMLRoot): """ Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the @@ -7899,7 +7899,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GeneToGeneCoexpressionAssociation(GeneToGeneAssociation): """ Indicates that two genes are co-expressed, generally under the same conditions. @@ -7912,11 +7912,11 @@ class GeneToGeneCoexpressionAssociation(GeneToGeneAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToGeneCoexpressionAssociation id: Union[str, GeneToGeneCoexpressionAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None expression_site: Optional[Union[str, AnatomicalEntityId]] = None stage_qualifier: Optional[Union[str, LifeStageId]] = None @@ -7951,7 +7951,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): """ An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between @@ -7965,11 +7965,11 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.PairwiseGeneToGeneInteraction id: Union[str, PairwiseGeneToGeneInteractionId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -7988,7 +7988,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): """ An interaction at the molecular level between two physical entities @@ -8001,11 +8001,11 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): class_model_uri: ClassVar[URIRef] = BIOLINK.PairwiseMolecularInteraction id: Union[str, PairwiseMolecularInteractionId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MolecularEntityId] = None predicate: Union[str, PredicateType] = None object: Union[str, MolecularEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" interacting_molecules_category: Optional[Union[str, OntologyClassId]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8038,7 +8038,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellLineToEntityAssociationMixin(YAMLRoot): """ An relationship between a cell line and another entity @@ -8073,7 +8073,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class CellLineToDiseaseOrPhenotypicFeatureAssociation(Association): """ An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an @@ -8089,9 +8089,9 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(Association): id: Union[str, CellLineToDiseaseOrPhenotypicFeatureAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, DiseaseOrPhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8120,7 +8120,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalEntityToEntityAssociationMixin(YAMLRoot): """ An interaction between a chemical entity and another entity @@ -8155,7 +8155,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DrugToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): """ An interaction between a drug and another entity @@ -8195,7 +8195,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class ChemicalToEntityAssociationMixin(ChemicalEntityToEntityAssociationMixin): """ An interaction between a chemical entity and another entity @@ -8235,7 +8235,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class CaseToEntityAssociationMixin(YAMLRoot): """ An abstract association for use where the case is the subject @@ -8270,7 +8270,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class ChemicalToChemicalAssociation(Association): """ A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal @@ -8284,11 +8284,11 @@ class ChemicalToChemicalAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalToChemicalAssociation id: Union[str, ChemicalToChemicalAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, ChemicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8317,7 +8317,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -8327,11 +8327,11 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.ReactionToParticipantAssociation id: Union[str, ReactionToParticipantAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, ChemicalEntityId] = None subject: Union[str, MolecularEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" stoichiometry: Optional[int] = None reaction_direction: Optional[Union[str, "ReactionDirectionEnum"]] = None reaction_side: Optional[Union[str, "ReactionSideEnum"]] = None @@ -8362,7 +8362,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ReactionToCatalystAssociation(ReactionToParticipantAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -8372,11 +8372,11 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.ReactionToCatalystAssociation id: Union[str, ReactionToCatalystAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, MolecularEntityId] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8395,7 +8395,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): """ A causal relationship between two chemical entities, where the subject represents the upstream entity and the @@ -8410,11 +8410,11 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalToChemicalDerivationAssociation id: Union[str, ChemicalToChemicalDerivationAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None object: Union[str, ChemicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" catalyst_qualifier: Optional[Union[Union[dict, MacromolecularMachineMixin], List[Union[dict, MacromolecularMachineMixin]]]] = empty_list() def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8448,7 +8448,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalToDiseaseOrPhenotypicFeatureAssociation(Association): """ An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise @@ -8464,9 +8464,9 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(Association): id: Union[str, ChemicalToDiseaseOrPhenotypicFeatureAssociationId] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, DiseaseOrPhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8495,7 +8495,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(Association): """ This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic @@ -8511,9 +8511,9 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(Associati id: Union[str, ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociationId] = None subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" FDA_adverse_event_level: Optional[Union[str, "FDAIDAAdverseEventEnum"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8546,7 +8546,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation): """ This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic @@ -8562,9 +8562,9 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C id: Union[str, ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociationId] = None subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8593,7 +8593,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToPathwayAssociation(Association): """ An interaction between a gene or gene product and a biological process or pathway. @@ -8607,10 +8607,10 @@ class GeneToPathwayAssociation(Association): id: Union[str, GeneToPathwayAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, PathwayId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8639,7 +8639,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularActivityToPathwayAssociation(Association): """ Association that holds the relationship between a reaction and the pathway it participates in. @@ -8652,11 +8652,11 @@ class MolecularActivityToPathwayAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.MolecularActivityToPathwayAssociation id: Union[str, MolecularActivityToPathwayAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MolecularActivityId] = None object: Union[str, PathwayId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8685,7 +8685,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalToPathwayAssociation(Association): """ An interaction between a chemical entity and a biological process or pathway. @@ -8699,10 +8699,10 @@ class ChemicalToPathwayAssociation(Association): id: Union[str, ChemicalToPathwayAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None object: Union[str, PathwayId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8731,7 +8731,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -8741,11 +8741,11 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.NamedThingAssociatedWithLikelihoodOfNamedThingAssociation id: Union[str, NamedThingAssociatedWithLikelihoodOfNamedThingAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_aspect_qualifier: Optional[str] = None subject_context_qualifier: Optional[Union[str, OntologyClassId]] = None object_aspect_qualifier: Optional[str] = None @@ -8794,7 +8794,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalGeneInteractionAssociation(Association): """ describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical @@ -8809,11 +8809,11 @@ class ChemicalGeneInteractionAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalGeneInteractionAssociation id: Union[str, ChemicalGeneInteractionAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None object: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[Union[str, "ChemicalOrGeneOrGeneProductFormOrVariantEnum"]] = None subject_part_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalPartQualifierEnum"]] = None subject_derivative_qualifier: Optional[Union[str, "ChemicalEntityDerivativeEnum"]] = None @@ -8874,7 +8874,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneRegulatesGeneAssociation(Association): """ Describes a regulatory relationship between two genes or gene products. @@ -8887,14 +8887,14 @@ class GeneRegulatesGeneAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneRegulatesGeneAssociation id: Union[str, GeneRegulatesGeneAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object_aspect_qualifier: Union[str, "GeneOrGeneProductOrChemicalEntityAspectEnum"] = None object_direction_qualifier: Union[str, "DirectionQualifierEnum"] = None qualified_predicate: str = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" species_context_qualifier: Optional[Union[str, OrganismTaxonId]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -8942,7 +8942,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ProcessRegulatesProcessAssociation(Association): """ Describes a regulatory relationship between two genes or gene products. @@ -8955,11 +8955,11 @@ class ProcessRegulatesProcessAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ProcessRegulatesProcessAssociation id: Union[str, ProcessRegulatesProcessAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, BiologicalProcessId] = None predicate: Union[str, PredicateType] = None object: Union[str, BiologicalProcessId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -8988,7 +8988,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalAffectsGeneAssociation(Association): """ Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, @@ -9002,11 +9002,11 @@ class ChemicalAffectsGeneAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalAffectsGeneAssociation id: Union[str, ChemicalAffectsGeneAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ChemicalEntityId] = None predicate: Union[str, PredicateType] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[Union[str, "ChemicalOrGeneOrGeneProductFormOrVariantEnum"]] = None subject_part_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalPartQualifierEnum"]] = None subject_derivative_qualifier: Optional[Union[str, "ChemicalEntityDerivativeEnum"]] = None @@ -9095,7 +9095,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneAffectsChemicalAssociation(Association): """ Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, @@ -9109,11 +9109,11 @@ class GeneAffectsChemicalAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneAffectsChemicalAssociation id: Union[str, GeneAffectsChemicalAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None object: Union[str, ChemicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[Union[str, "ChemicalOrGeneOrGeneProductFormOrVariantEnum"]] = None subject_part_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalPartQualifierEnum"]] = None subject_derivative_qualifier: Optional[str] = None @@ -9206,7 +9206,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DrugToGeneAssociation(Association): """ An interaction between a drug and a gene or gene product. @@ -9221,9 +9221,9 @@ class DrugToGeneAssociation(Association): id: Union[str, DrugToGeneAssociationId] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9252,7 +9252,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MaterialSampleToEntityAssociationMixin(YAMLRoot): """ An association between a material sample and something. @@ -9287,7 +9287,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class MaterialSampleDerivationAssociation(Association): """ An association between a material sample and the material entity from which it is derived. @@ -9300,11 +9300,11 @@ class MaterialSampleDerivationAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.MaterialSampleDerivationAssociation id: Union[str, MaterialSampleDerivationAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MaterialSampleId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9333,7 +9333,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(Association): """ An association between a material sample and a disease or phenotype. @@ -9349,8 +9349,8 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9379,7 +9379,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -9411,7 +9411,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class EntityToExposureEventAssociationMixin(YAMLRoot): """ An association between some entity and an exposure event. @@ -9446,7 +9446,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DiseaseToExposureEventAssociation(Association): """ An association between an exposure event and a disease. @@ -9462,8 +9462,8 @@ class DiseaseToExposureEventAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9492,7 +9492,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToOutcomeAssociationMixin(YAMLRoot): """ An association between some entity and an outcome @@ -9527,7 +9527,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class ExposureEventToOutcomeAssociation(Association): """ An association between an exposure event and an outcome. @@ -9543,8 +9543,8 @@ class ExposureEventToOutcomeAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None population_context_qualifier: Optional[Union[str, PopulationOfIndividualOrganismsId]] = None temporal_context_qualifier: Optional[Union[str, TimeType]] = None @@ -9581,7 +9581,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class FrequencyQualifierMixin(YAMLRoot): """ Qualifier for frequency type associations @@ -9620,7 +9620,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class EntityToFeatureOrDiseaseQualifiersMixin(FrequencyQualifierMixin): """ Qualifiers for entity to disease or phenotype associations. @@ -9660,7 +9660,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class FeatureOrDiseaseQualifiersToEntityMixin(FrequencyQualifierMixin): """ Qualifiers for disease or phenotype to entity associations. @@ -9700,7 +9700,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class EntityToPhenotypicFeatureAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin): _inherited_slots: ClassVar[List[str]] = [] @@ -9752,7 +9752,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class PhenotypicFeatureToEntityAssociationMixin(FeatureOrDiseaseQualifiersToEntityMixin): _inherited_slots: ClassVar[List[str]] = [] @@ -9794,7 +9794,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class PhenotypicFeatureToPhenotypicFeatureAssociation(Association): """ Association between two concept nodes of phenotypic character, qualified by the predicate used. This association @@ -9811,8 +9811,8 @@ class PhenotypicFeatureToPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -9869,7 +9869,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class InformationContentEntityToNamedThingAssociation(Association): """ association between a named thing and a information content entity where the specific context of the relationship @@ -9887,11 +9887,11 @@ class InformationContentEntityToNamedThingAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.InformationContentEntityToNamedThingAssociation id: Union[str, InformationContentEntityToNamedThingAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -9920,7 +9920,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToDiseaseAssociationMixin(EntityToFeatureOrDiseaseQualifiersMixin): """ mixin class for any association whose object (target node) is a disease @@ -9945,7 +9945,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeatureToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -9977,7 +9977,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeatureToLocationAssociation(Association): """ An association between either a disease or a phenotypic feature and an anatomical entity, where the @@ -9993,9 +9993,9 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(Association): id: Union[str, DiseaseOrPhenotypicFeatureToLocationAssociationId] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, AnatomicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10024,7 +10024,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(Association): """ An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance. @@ -10038,10 +10038,10 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(Association): id: Union[str, DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociationId] = None subject: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, GeneticInheritanceId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -10070,7 +10070,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToDiseaseOrPhenotypicFeatureAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10102,7 +10102,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GenotypeToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10134,7 +10134,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GenotypeToPhenotypicFeatureAssociation(Association): """ Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, @@ -10149,10 +10149,10 @@ class GenotypeToPhenotypicFeatureAssociation(Association): id: Union[str, GenotypeToPhenotypicFeatureAssociationId] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[str, GenotypeId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10209,7 +10209,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ExposureEventToPhenotypicFeatureAssociation(Association): """ Any association between an environment and a phenotypic feature, where being in the environment influences the @@ -10225,9 +10225,9 @@ class ExposureEventToPhenotypicFeatureAssociation(Association): id: Union[str, ExposureEventToPhenotypicFeatureAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ExposureEventId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10284,7 +10284,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DiseaseToPhenotypicFeatureAssociation(Association): """ An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the @@ -10299,10 +10299,10 @@ class DiseaseToPhenotypicFeatureAssociation(Association): id: Union[str, DiseaseToPhenotypicFeatureAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, DiseaseId] = None object: Union[str, PhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" onset_qualifier: Optional[Union[str, OnsetId]] = None has_count: Optional[int] = None has_total: Optional[int] = None @@ -10379,7 +10379,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CaseToPhenotypicFeatureAssociation(Association): """ An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or @@ -10396,8 +10396,8 @@ class CaseToPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10454,7 +10454,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class BehaviorToBehavioralFeatureAssociation(Association): """ An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has @@ -10469,10 +10469,10 @@ class BehaviorToBehavioralFeatureAssociation(Association): id: Union[str, BehaviorToBehavioralFeatureAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, BehaviorId] = None object: Union[str, BehavioralFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -10529,7 +10529,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10561,7 +10561,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class VariantToEntityAssociationMixin(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] @@ -10593,7 +10593,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GeneToDiseaseOrPhenotypicFeatureAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -10603,11 +10603,11 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToDiseaseOrPhenotypicFeatureAssociation id: Union[str, GeneToDiseaseOrPhenotypicFeatureAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseOrPhenotypicFeatureId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_aspect_qualifier: Optional[Union[str, "GeneOrGeneProductOrChemicalEntityAspectEnum"]] = None object_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None frequency_qualifier: Optional[Union[str, FrequencyValue]] = None @@ -10664,7 +10664,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10674,11 +10674,11 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToPhenotypicFeatureAssociation id: Union[str, GeneToPhenotypicFeatureAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, PhenotypicFeatureId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10722,7 +10722,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10732,11 +10732,11 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToDiseaseAssociation id: Union[str, GeneToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10776,7 +10776,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10786,11 +10786,11 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.CausalGeneToDiseaseAssociation id: Union[str, CausalGeneToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10830,7 +10830,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10840,11 +10840,11 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.CorrelatedGeneToDiseaseAssociation id: Union[str, CorrelatedGeneToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10884,7 +10884,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -10894,11 +10894,11 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.DruggableGeneToDiseaseAssociation id: Union[str, DruggableGeneToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, DiseaseId] = None subject: Union[dict, GeneOrGeneProduct] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -10943,7 +10943,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PhenotypicFeatureToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -10955,9 +10955,9 @@ class PhenotypicFeatureToDiseaseAssociation(Association): id: Union[str, PhenotypicFeatureToDiseaseAssociationId] = None subject: Union[str, NamedThingId] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11014,7 +11014,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToGeneAssociation(Association): """ An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in @@ -11029,10 +11029,10 @@ class VariantToGeneAssociation(Association): id: Union[str, VariantToGeneAssociationId] = None subject: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, GeneId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11061,7 +11061,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToGeneExpressionAssociation(VariantToGeneAssociation): """ An association between a variant and expression of a gene (i.e. e-QTL) @@ -11075,10 +11075,10 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation): id: Union[str, VariantToGeneExpressionAssociationId] = None subject: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None object: Union[str, GeneId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None expression_site: Optional[Union[str, AnatomicalEntityId]] = None stage_qualifier: Optional[Union[str, LifeStageId]] = None @@ -11113,7 +11113,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToPopulationAssociation(Association): """ An association between a variant and a population, where the variant has particular frequency in the population @@ -11127,10 +11127,10 @@ class VariantToPopulationAssociation(Association): id: Union[str, VariantToPopulationAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, SequenceVariantId] = None object: Union[str, PopulationOfIndividualOrganismsId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" has_quotient: Optional[float] = None has_count: Optional[int] = None has_total: Optional[int] = None @@ -11179,7 +11179,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class PopulationToPopulationAssociation(Association): """ An association between a two populations @@ -11192,11 +11192,11 @@ class PopulationToPopulationAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.PopulationToPopulationAssociation id: Union[str, PopulationToPopulationAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, PopulationOfIndividualOrganismsId] = None object: Union[str, PopulationOfIndividualOrganismsId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11225,7 +11225,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToPhenotypicFeatureAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11237,9 +11237,9 @@ class VariantToPhenotypicFeatureAssociation(Association): id: Union[str, VariantToPhenotypicFeatureAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, SequenceVariantId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11296,7 +11296,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11306,11 +11306,11 @@ class VariantToDiseaseAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.VariantToDiseaseAssociation id: Union[str, VariantToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11363,7 +11363,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11373,11 +11373,11 @@ class GenotypeToDiseaseAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeToDiseaseAssociation id: Union[str, GenotypeToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11430,7 +11430,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ModelToDiseaseAssociationMixin(YAMLRoot): """ This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in @@ -11467,7 +11467,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class GeneAsAModelOfDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11477,11 +11477,11 @@ class GeneAsAModelOfDiseaseAssociation(GeneToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneAsAModelOfDiseaseAssociation id: Union[str, GeneAsAModelOfDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, DiseaseId] = None subject: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None object_aspect_qualifier: Optional[str] = None @@ -11516,7 +11516,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class VariantAsAModelOfDiseaseAssociation(VariantToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11526,11 +11526,11 @@ class VariantAsAModelOfDiseaseAssociation(VariantToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.VariantAsAModelOfDiseaseAssociation id: Union[str, VariantAsAModelOfDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, SequenceVariantId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11573,7 +11573,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenotypeAsAModelOfDiseaseAssociation(GenotypeToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11583,11 +11583,11 @@ class GenotypeAsAModelOfDiseaseAssociation(GenotypeToDiseaseAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GenotypeAsAModelOfDiseaseAssociation id: Union[str, GenotypeAsAModelOfDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None subject: Union[str, GenotypeId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11630,7 +11630,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class CellLineAsAModelOfDiseaseAssociation(CellLineToDiseaseOrPhenotypicFeatureAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11642,9 +11642,9 @@ class CellLineAsAModelOfDiseaseAssociation(CellLineToDiseaseOrPhenotypicFeatureA id: Union[str, CellLineAsAModelOfDiseaseAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, CellLineId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11697,7 +11697,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismalEntityAsAModelOfDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11709,9 +11709,9 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(Association): id: Union[str, OrganismalEntityAsAModelOfDiseaseAssociationId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" frequency_qualifier: Optional[Union[str, FrequencyValue]] = None subject_aspect_qualifier: Optional[str] = None subject_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None @@ -11764,7 +11764,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismToOrganismAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11775,10 +11775,10 @@ class OrganismToOrganismAssociation(Association): id: Union[str, OrganismToOrganismAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, IndividualOrganismId] = None object: Union[str, IndividualOrganismId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11802,7 +11802,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class TaxonToTaxonAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -11813,10 +11813,10 @@ class TaxonToTaxonAssociation(Association): id: Union[str, TaxonToTaxonAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -11840,7 +11840,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -11850,11 +11850,11 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation class_model_uri: ClassVar[URIRef] = BIOLINK.GeneHasVariantThatContributesToDiseaseAssociation id: Union[str, GeneHasVariantThatContributesToDiseaseAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, DiseaseId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" subject_form_or_variant_qualifier: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -11887,7 +11887,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToExpressionSiteAssociation(Association): """ An association between a gene and a gene expression site, possibly qualified by stage/timing info. @@ -11900,11 +11900,11 @@ class GeneToExpressionSiteAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToExpressionSiteAssociation id: Union[str, GeneToExpressionSiteAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, GeneOrGeneProduct] = None object: Union[str, AnatomicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" stage_qualifier: Optional[Union[str, LifeStageId]] = None quantifier_qualifier: Optional[Union[str, OntologyClassId]] = None @@ -11941,7 +11941,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SequenceVariantModulatesTreatmentAssociation(Association): """ An association between a sequence variant and a treatment or health intervention. The treatment object itself @@ -11956,10 +11956,10 @@ class SequenceVariantModulatesTreatmentAssociation(Association): id: Union[str, SequenceVariantModulatesTreatmentAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, SequenceVariantId] = None object: Union[str, TreatmentId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): @@ -11978,7 +11978,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class FunctionalAssociation(Association): """ An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either @@ -11993,10 +11993,10 @@ class FunctionalAssociation(Association): id: Union[str, FunctionalAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, OntologyClassId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12020,7 +12020,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MacromolecularMachineToEntityAssociationMixin(YAMLRoot): """ an association which has a macromolecular machine mixin as a subject @@ -12055,7 +12055,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class MacromolecularMachineToMolecularActivityAssociation(FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity @@ -12071,10 +12071,10 @@ class MacromolecularMachineToMolecularActivityAssociation(FunctionalAssociation) id: Union[str, MacromolecularMachineToMolecularActivityAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, MolecularActivityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12098,7 +12098,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MacromolecularMachineToBiologicalProcessAssociation(FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a biological process @@ -12114,10 +12114,10 @@ class MacromolecularMachineToBiologicalProcessAssociation(FunctionalAssociation) id: Union[str, MacromolecularMachineToBiologicalProcessAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, BiologicalProcessId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12141,7 +12141,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MacromolecularMachineToCellularComponentAssociation(FunctionalAssociation): """ A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component @@ -12157,10 +12157,10 @@ class MacromolecularMachineToCellularComponentAssociation(FunctionalAssociation) id: Union[str, MacromolecularMachineToCellularComponentAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[dict, MacromolecularMachineMixin] = None object: Union[str, CellularComponentId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12184,7 +12184,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularActivityToChemicalEntityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood @@ -12199,10 +12199,10 @@ class MolecularActivityToChemicalEntityAssociation(Association): id: Union[str, MolecularActivityToChemicalEntityAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MolecularActivityId] = None object: Union[str, ChemicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12226,7 +12226,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class MolecularActivityToMolecularActivityAssociation(Association): """ Added in response to capturing relationship between microbiome activities as measured via measurements of blood @@ -12241,10 +12241,10 @@ class MolecularActivityToMolecularActivityAssociation(Association): id: Union[str, MolecularActivityToMolecularActivityAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, MolecularActivityId] = None object: Union[str, MolecularActivityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12268,7 +12268,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGoTermAssociation(FunctionalAssociation): _inherited_slots: ClassVar[List[str]] = [] @@ -12279,10 +12279,10 @@ class GeneToGoTermAssociation(FunctionalAssociation): id: Union[str, GeneToGoTermAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, GeneId] = None object: Union[str, OntologyClassId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12306,7 +12306,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToDiseaseAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -12319,8 +12319,8 @@ class EntityToDiseaseAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None clinical_approval_status: Optional[Union[str, "ClinicalApprovalStatusEnum"]] = None max_research_phase: Optional[Union[str, "ResearchPhaseEnum"]] = None @@ -12342,7 +12342,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class EntityToPhenotypicFeatureAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -12355,8 +12355,8 @@ class EntityToPhenotypicFeatureAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None clinical_approval_status: Optional[Union[str, "ClinicalApprovalStatusEnum"]] = None max_research_phase: Optional[Union[str, "ResearchPhaseEnum"]] = None @@ -12378,7 +12378,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SequenceAssociation(Association): """ An association between a sequence feature and a nucleic acid entity it is localized to. @@ -12394,8 +12394,8 @@ class SequenceAssociation(Association): subject: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None object: Union[str, NamedThingId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12409,7 +12409,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GenomicSequenceLocalization(SequenceAssociation): """ A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may @@ -12423,11 +12423,11 @@ class GenomicSequenceLocalization(SequenceAssociation): class_model_uri: ClassVar[URIRef] = BIOLINK.GenomicSequenceLocalization id: Union[str, GenomicSequenceLocalizationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NucleicAcidEntityId] = None object: Union[str, NucleicAcidEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" start_interbase_coordinate: Optional[int] = None end_interbase_coordinate: Optional[int] = None genome_build: Optional[Union[str, "StrandEnum"]] = None @@ -12476,7 +12476,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class SequenceFeatureRelationship(Association): """ For example, a particular exon is part of a particular transcript or gene @@ -12490,10 +12490,10 @@ class SequenceFeatureRelationship(Association): id: Union[str, SequenceFeatureRelationshipId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, NucleicAcidEntityId] = None object: Union[str, NucleicAcidEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12517,7 +12517,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class TranscriptToGeneRelationship(SequenceFeatureRelationship): """ A gene is a collection of transcripts @@ -12531,10 +12531,10 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): id: Union[str, TranscriptToGeneRelationshipId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, TranscriptId] = None object: Union[str, GeneId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12558,7 +12558,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class GeneToGeneProductRelationship(SequenceFeatureRelationship): """ A gene is transcribed and potentially translated to a gene product @@ -12571,11 +12571,11 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): class_model_uri: ClassVar[URIRef] = BIOLINK.GeneToGeneProductRelationship id: Union[str, GeneToGeneProductRelationshipId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, GeneId] = None object: Union[dict, GeneProductMixin] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12604,7 +12604,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ExonToTranscriptRelationship(SequenceFeatureRelationship): """ A transcript is formed from multiple exons @@ -12618,10 +12618,10 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): id: Union[str, ExonToTranscriptRelationshipId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, ExonId] = None object: Union[str, TranscriptId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12645,7 +12645,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): """ A regulatory relationship between two genes @@ -12658,11 +12658,11 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation id: Union[str, ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None predicate: Union[str, PredicateType] = None subject: Union[dict, ChemicalEntityOrGeneOrGeneProduct] = None object: Union[dict, GeneOrGeneProduct] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" object_direction_qualifier: Optional[Union[str, "DirectionQualifierEnum"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -12695,7 +12695,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AnatomicalEntityToAnatomicalEntityAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -12706,10 +12706,10 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): id: Union[str, AnatomicalEntityToAnatomicalEntityAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, AnatomicalEntityId] = None object: Union[str, AnatomicalEntityId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): @@ -12728,7 +12728,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnatomicalEntityAssociation): """ A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are @@ -12743,11 +12743,11 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat class_model_uri: ClassVar[URIRef] = BIOLINK.AnatomicalEntityToAnatomicalEntityPartOfAssociation id: Union[str, AnatomicalEntityToAnatomicalEntityPartOfAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, AnatomicalEntityId] = None object: Union[str, AnatomicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12776,7 +12776,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToAnatomicalEntityAssociation): """ A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are @@ -12791,11 +12791,11 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA class_model_uri: ClassVar[URIRef] = BIOLINK.AnatomicalEntityToAnatomicalEntityOntogenicAssociation id: Union[str, AnatomicalEntityToAnatomicalEntityOntogenicAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, AnatomicalEntityId] = None object: Union[str, AnatomicalEntityId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12824,7 +12824,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismTaxonToEntityAssociation(YAMLRoot): """ An association between an organism taxon and another entity @@ -12859,7 +12859,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class OrganismTaxonToOrganismTaxonAssociation(Association): """ A relationship between two organism taxon nodes @@ -12873,10 +12873,10 @@ class OrganismTaxonToOrganismTaxonAssociation(Association): id: Union[str, OrganismTaxonToOrganismTaxonAssociationId] = None predicate: Union[str, PredicateType] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.predicate): @@ -12900,7 +12900,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAssociation): """ A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo @@ -12913,11 +12913,11 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss class_model_uri: ClassVar[URIRef] = BIOLINK.OrganismTaxonToOrganismTaxonSpecialization id: Union[str, OrganismTaxonToOrganismTaxonSpecializationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.id): @@ -12946,7 +12946,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssociation): """ An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and @@ -12961,11 +12961,11 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci class_model_uri: ClassVar[URIRef] = BIOLINK.OrganismTaxonToOrganismTaxonInteraction id: Union[str, OrganismTaxonToOrganismTaxonInteractionId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, OrganismTaxonId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" associated_environmental_context: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): @@ -12998,7 +12998,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.category = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.category] -@dataclass +@dataclass(repr=False) class OrganismTaxonToEnvironmentAssociation(Association): _inherited_slots: ClassVar[List[str]] = [] @@ -13008,11 +13008,11 @@ class OrganismTaxonToEnvironmentAssociation(Association): class_model_uri: ClassVar[URIRef] = BIOLINK.OrganismTaxonToEnvironmentAssociation id: Union[str, OrganismTaxonToEnvironmentAssociationId] = None + knowledge_level: Union[str, "KnowledgeLevelEnum"] = None + agent_type: Union[str, "AgentTypeEnum"] = None subject: Union[str, OrganismTaxonId] = None object: Union[str, NamedThingId] = None predicate: Union[str, PredicateType] = None - knowledge_level: Union[str, "KnowledgeLevelEnum"] = "not_provided" - agent_type: Union[str, "AgentTypeEnum"] = "not_provided" def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self._is_empty(self.subject): diff --git a/src/biolink_model/datamodel/pydanticmodel_v2.py b/src/biolink_model/datamodel/pydanticmodel_v2.py index 89df2655e..8ed903c96 100644 --- a/src/biolink_model/datamodel/pydanticmodel_v2.py +++ b/src/biolink_model/datamodel/pydanticmodel_v2.py @@ -1,7 +1,8 @@ from __future__ import annotations from datetime import ( datetime, - date + date, + time ) from decimal import Decimal from enum import Enum @@ -9,44 +10,57 @@ import sys from typing import ( Any, + ClassVar, List, Literal, Dict, Optional, Union ) -from pydantic.version import VERSION as PYDANTIC_VERSION -if int(PYDANTIC_VERSION[0])>=2: - from pydantic import ( - BaseModel, - ConfigDict, - Field, - field_validator - ) -else: - from pydantic import ( - BaseModel, - Field, - validator - ) - +from pydantic import ( + BaseModel, + ConfigDict, + Field, + RootModel, + field_validator +) metamodel_version = "None" version = "4.2.4" -class WeakRefShimBaseModel(BaseModel): - __slots__ = '__weakref__' - -class ConfiguredBaseModel(WeakRefShimBaseModel, - validate_assignment = True, - validate_all = True, - underscore_attrs_are_private = True, - extra = "forbid", - arbitrary_types_allowed = True, - use_enum_values = True): +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + validate_assignment = True, + validate_default = True, + extra = "forbid", + arbitrary_types_allowed = True, + use_enum_values = True, + strict = False, + ) pass + + +class LinkMLMeta(RootModel): + root: Dict[str, Any] = {} + model_config = ConfigDict(frozen=True) + + def __getattr__(self, key:str): + return getattr(self.root, key) + + def __getitem__(self, key:str): + return self.root[key] + + def __setitem__(self, key:str, value): + self.root[key] = value + + def __contains__(self, key:str) -> bool: + return key in self.root + + +linkml_meta = None + class ApprovalStatusEnum(str, Enum): # Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments. discovery_and_development_phase = "discovery_and_development_phase" @@ -364,6 +378,7 @@ class KnowledgeLevelEnum(str, Enum): not_provided = "not_provided" + class MappingCollection(ConfiguredBaseModel): """ A collection of deprecated mappings. @@ -457,7 +472,7 @@ class Entity(ConfiguredBaseModel): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Entity","biolink:Entity"]] = Field(["biolink:Entity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -469,13 +484,13 @@ class NamedThing(Entity): a databased entity or concept/class """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NamedThing","biolink:NamedThing"]] = Field(["biolink:NamedThing"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -493,11 +508,11 @@ class Attribute(NamedThing, OntologyClass): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/Attribute","biolink:Attribute"]] = Field(["biolink:Attribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -514,11 +529,11 @@ class ChemicalRole(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalRole","biolink:ChemicalRole"]] = Field(["biolink:ChemicalRole"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -532,11 +547,11 @@ class BiologicalSex(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalSex","biolink:BiologicalSex"]] = Field(["biolink:BiologicalSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -553,11 +568,11 @@ class PhenotypicSex(BiologicalSex): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicSex","biolink:PhenotypicSex"]] = Field(["biolink:PhenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -574,11 +589,11 @@ class GenotypicSex(BiologicalSex): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypicSex","biolink:GenotypicSex"]] = Field(["biolink:GenotypicSex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -595,11 +610,11 @@ class SeverityValue(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/SeverityValue","biolink:SeverityValue"]] = Field(["biolink:SeverityValue"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -625,13 +640,13 @@ class OrganismTaxon(NamedThing): """ has_taxonomic_rank: Optional[str] = Field(None) provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxon","biolink:OrganismTaxon"]] = Field(["biolink:OrganismTaxon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -643,13 +658,13 @@ class Event(NamedThing): Something that happens at a given place and time. """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Event","biolink:Event"]] = Field(["biolink:Event"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -658,13 +673,13 @@ class Event(NamedThing): class AdministrativeEntity(NamedThing): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AdministrativeEntity","biolink:AdministrativeEntity"]] = Field(["biolink:AdministrativeEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -675,16 +690,16 @@ class Agent(AdministrativeEntity): """ person, group, organization or project that provides a piece of information (i.e. a knowledge association) """ - affiliation: Optional[List[str]] = Field(default_factory=list, description="""a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.""") + affiliation: Optional[List[str]] = Field(None, description="""a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.""") address: Optional[str] = Field(None, description="""the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?).""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Agent","biolink:Agent"]] = Field(["biolink:Agent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -700,13 +715,13 @@ class InformationContentEntity(NamedThing): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/InformationContentEntity","biolink:InformationContentEntity"]] = Field(["biolink:InformationContentEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -722,13 +737,13 @@ class StudyResult(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyResult","biolink:StudyResult"]] = Field(["biolink:StudyResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -744,13 +759,13 @@ class StudyVariable(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyVariable","biolink:StudyVariable"]] = Field(["biolink:StudyVariable"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -766,13 +781,13 @@ class CommonDataElement(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CommonDataElement","biolink:CommonDataElement"]] = Field(["biolink:CommonDataElement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -788,13 +803,13 @@ class ConceptCountAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ConceptCountAnalysisResult","biolink:ConceptCountAnalysisResult"]] = Field(["biolink:ConceptCountAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -810,13 +825,13 @@ class ObservedExpectedFrequencyAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ObservedExpectedFrequencyAnalysisResult","biolink:ObservedExpectedFrequencyAnalysisResult"]] = Field(["biolink:ObservedExpectedFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -832,13 +847,13 @@ class RelativeFrequencyAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RelativeFrequencyAnalysisResult","biolink:RelativeFrequencyAnalysisResult"]] = Field(["biolink:RelativeFrequencyAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -854,13 +869,13 @@ class TextMiningResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TextMiningResult","biolink:TextMiningResult"]] = Field(["biolink:TextMiningResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -876,13 +891,13 @@ class ChiSquaredAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChiSquaredAnalysisResult","biolink:ChiSquaredAnalysisResult"]] = Field(["biolink:ChiSquaredAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -898,13 +913,13 @@ class LogOddsAnalysisResult(StudyResult): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/LogOddsAnalysisResult","biolink:LogOddsAnalysisResult"]] = Field(["biolink:LogOddsAnalysisResult"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -920,13 +935,13 @@ class Dataset(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Dataset","biolink:Dataset"]] = Field(["biolink:Dataset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -943,13 +958,13 @@ class DatasetDistribution(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetDistribution","biolink:DatasetDistribution"]] = Field(["biolink:DatasetDistribution"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -968,13 +983,13 @@ class DatasetVersion(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetVersion","biolink:DatasetVersion"]] = Field(["biolink:DatasetVersion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -992,13 +1007,13 @@ class DatasetSummary(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DatasetSummary","biolink:DatasetSummary"]] = Field(["biolink:DatasetSummary"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1014,13 +1029,13 @@ class ConfidenceLevel(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ConfidenceLevel","biolink:ConfidenceLevel"]] = Field(["biolink:ConfidenceLevel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1036,13 +1051,13 @@ class EvidenceType(InformationContentEntity): format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EvidenceType","biolink:EvidenceType"]] = Field(["biolink:EvidenceType"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1053,12 +1068,12 @@ class Publication(InformationContentEntity): """ Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1066,11 +1081,11 @@ class Publication(InformationContentEntity): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Publication","biolink:Publication"]] = Field(["biolink:Publication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1081,12 +1096,12 @@ class Book(Publication): """ This class may rarely be instantiated except if use cases of a given knowledge graph support its utility. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1094,11 +1109,11 @@ class Book(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Books should have industry-standard identifier such as from ISBN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Book","biolink:Book"]] = Field(["biolink:Book"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'book'.""") + type: Optional[List[str]] = Field(None, description="""Should generally be set to an ontology class defined term for 'book'.""") name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1109,12 +1124,12 @@ class BookChapter(Publication): published_in: str = Field(..., description="""The enclosing parent book containing the chapter should have industry-standard identifier from ISBN.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") chapter: Optional[str] = Field(None, description="""chapter of a book""") - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1122,11 +1137,11 @@ class BookChapter(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BookChapter","biolink:BookChapter"]] = Field(["biolink:BookChapter"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1140,12 +1155,12 @@ class Serial(Publication): iso_abbreviation: Optional[str] = Field(None, description="""Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1153,11 +1168,11 @@ class Serial(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Serials (journals) should have industry-standard identifier such as from ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Serial","biolink:Serial"]] = Field(["biolink:Serial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""Should generally be set to an ontology class defined term for 'serial' or 'journal'.""") + type: Optional[List[str]] = Field(None, description="""Should generally be set to an ontology class defined term for 'serial' or 'journal'.""") name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1172,12 +1187,12 @@ class Article(Publication): iso_abbreviation: Optional[str] = Field(None, description="""Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1185,11 +1200,11 @@ class Article(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Article","biolink:Article"]] = Field(["biolink:Article"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1204,12 +1219,12 @@ class JournalArticle(Article): iso_abbreviation: Optional[str] = Field(None, description="""Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent.""") volume: Optional[str] = Field(None, description="""volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication""") issue: Optional[str] = Field(None, description="""issue of a newspaper, a scientific journal or magazine for reference purpose""") - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1217,11 +1232,11 @@ class JournalArticle(Article): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/JournalArticle","biolink:JournalArticle"]] = Field(["biolink:JournalArticle"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1232,12 +1247,12 @@ class Patent(Publication): """ a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1245,11 +1260,11 @@ class Patent(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Patent","biolink:Patent"]] = Field(["biolink:Patent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1260,12 +1275,12 @@ class WebPage(Publication): """ a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1273,11 +1288,11 @@ class WebPage(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/WebPage","biolink:WebPage"]] = Field(["biolink:WebPage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1288,12 +1303,12 @@ class PreprintPublication(Publication): """ a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1301,11 +1316,11 @@ class PreprintPublication(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PreprintPublication","biolink:PreprintPublication"]] = Field(["biolink:PreprintPublication"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1316,12 +1331,12 @@ class DrugLabel(Publication): """ a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc. """ - authors: Optional[List[str]] = Field(default_factory=list, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") - pages: Optional[List[str]] = Field(default_factory=list, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") + authors: Optional[List[str]] = Field(None, description="""connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication.""") + pages: Optional[List[str]] = Field(None, description="""When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book.""") summary: Optional[str] = Field(None, description="""executive summary of a publication""") - keywords: Optional[List[str]] = Field(default_factory=list, description="""keywords tagging a publication""") + keywords: Optional[List[str]] = Field(None, description="""keywords tagging a publication""") mesh_terms: Optional[List[str]] = Field(None, description="""mesh terms tagging a publication""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") publication_type: List[str] = Field(..., description="""Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) @@ -1329,11 +1344,11 @@ class DrugLabel(Publication): creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DrugLabel","biolink:DrugLabel"]] = Field(["biolink:DrugLabel"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case).""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1347,18 +1362,18 @@ class RetrievalSource(InformationContentEntity): resource_id: str = Field(..., description="""The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") resource_role: ResourceRoleEnum = Field(..., description="""The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge.""") upstream_resource_ids: Optional[str] = Field(None, description="""The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") license: Optional[str] = Field(None) rights: Optional[str] = Field(None) format: Optional[str] = Field(None) creation_date: Optional[date] = Field(None, description="""date on which an entity was created. This can be applied to nodes or edges""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RetrievalSource","biolink:RetrievalSource"]] = Field(["biolink:RetrievalSource"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1384,13 +1399,13 @@ class PhysicalEntity(PhysicalEssence, NamedThing): An entity that has material reality (a.k.a. physical essence). """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhysicalEntity","biolink:PhysicalEntity"]] = Field(["biolink:PhysicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1416,13 +1431,13 @@ class Activity(ActivityAndBehavior, NamedThing): An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Activity","biolink:Activity"]] = Field(["biolink:Activity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1434,13 +1449,13 @@ class Study(Activity): a detailed investigation and/or analysis """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Study","biolink:Study"]] = Field(["biolink:Study"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1452,13 +1467,13 @@ class Procedure(ActivityAndBehavior, NamedThing): A series of actions conducted in a certain order or manner """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Procedure","biolink:Procedure"]] = Field(["biolink:Procedure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1470,13 +1485,13 @@ class Phenomenon(Occurrent, NamedThing): a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Phenomenon","biolink:Phenomenon"]] = Field(["biolink:Phenomenon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1488,13 +1503,13 @@ class Device(NamedThing): A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Device","biolink:Device"]] = Field(["biolink:Device"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1506,13 +1521,13 @@ class DiagnosticAid(NamedThing): A device or substance used to help diagnose disease or injury """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiagnosticAid","biolink:DiagnosticAid"]] = Field(["biolink:DiagnosticAid"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1531,13 +1546,13 @@ class MaterialSample(SubjectOfInvestigation, PhysicalEntity): A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO] """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSample","biolink:MaterialSample"]] = Field(["biolink:MaterialSample"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1549,13 +1564,13 @@ class PlanetaryEntity(NamedThing): Any entity or process that exists at the level of the whole planet """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PlanetaryEntity","biolink:PlanetaryEntity"]] = Field(["biolink:PlanetaryEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1564,13 +1579,13 @@ class PlanetaryEntity(NamedThing): class EnvironmentalProcess(PlanetaryEntity, Occurrent): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalProcess","biolink:EnvironmentalProcess"]] = Field(["biolink:EnvironmentalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1579,13 +1594,13 @@ class EnvironmentalProcess(PlanetaryEntity, Occurrent): class EnvironmentalFeature(PlanetaryEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFeature","biolink:EnvironmentalFeature"]] = Field(["biolink:EnvironmentalFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1599,13 +1614,13 @@ class GeographicLocation(PlanetaryEntity): latitude: Optional[float] = Field(None, description="""latitude""") longitude: Optional[float] = Field(None, description="""longitude""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocation","biolink:GeographicLocation"]] = Field(["biolink:GeographicLocation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1620,13 +1635,13 @@ class GeographicLocationAtTime(GeographicLocation): latitude: Optional[float] = Field(None, description="""latitude""") longitude: Optional[float] = Field(None, description="""longitude""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicLocationAtTime","biolink:GeographicLocationAtTime"]] = Field(["biolink:GeographicLocationAtTime"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1645,13 +1660,13 @@ class BiologicalEntity(ThingWithTaxon, NamedThing): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalEntity","biolink:BiologicalEntity"]] = Field(["biolink:BiologicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1677,12 +1692,12 @@ class BiologicalProcessOrActivity(BiologicalEntity, Occurrent, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalProcessOrActivity","biolink:BiologicalProcessOrActivity"]] = Field(["biolink:BiologicalProcessOrActivity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1700,12 +1715,12 @@ class MolecularActivity(BiologicalProcessOrActivity, Occurrent, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivity","biolink:MolecularActivity"]] = Field(["biolink:MolecularActivity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1723,12 +1738,12 @@ class BiologicalProcess(BiologicalProcessOrActivity, Occurrent, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BiologicalProcess","biolink:BiologicalProcess"]] = Field(["biolink:BiologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1743,12 +1758,12 @@ class Pathway(BiologicalProcess, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Pathway","biolink:Pathway"]] = Field(["biolink:Pathway"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1763,12 +1778,12 @@ class PhysiologicalProcess(BiologicalProcess, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhysiologicalProcess","biolink:PhysiologicalProcess"]] = Field(["biolink:PhysiologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1783,12 +1798,12 @@ class Behavior(BiologicalProcess, ActivityAndBehavior, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Behavior","biolink:Behavior"]] = Field(["biolink:Behavior"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1806,11 +1821,11 @@ class OrganismAttribute(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismAttribute","biolink:OrganismAttribute"]] = Field(["biolink:OrganismAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -1827,11 +1842,11 @@ class PhenotypicQuality(OrganismAttribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicQuality","biolink:PhenotypicQuality"]] = Field(["biolink:PhenotypicQuality"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -1844,13 +1859,13 @@ class GeneticInheritance(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneticInheritance","biolink:GeneticInheritance"]] = Field(["biolink:GeneticInheritance"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -1864,13 +1879,13 @@ class OrganismalEntity(BiologicalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismalEntity","biolink:OrganismalEntity"]] = Field(["biolink:OrganismalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1884,13 +1899,13 @@ class Bacterium(OrganismalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Bacterium","biolink:Bacterium"]] = Field(["biolink:Bacterium"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1904,13 +1919,13 @@ class Virus(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Virus","biolink:Virus"]] = Field(["biolink:Virus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1921,13 +1936,13 @@ class CellularOrganism(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellularOrganism","biolink:CellularOrganism"]] = Field(["biolink:CellularOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1941,13 +1956,13 @@ class Mammal(CellularOrganism, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Mammal","biolink:Mammal"]] = Field(["biolink:Mammal"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1961,13 +1976,13 @@ class Human(Mammal, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Human","biolink:Human"]] = Field(["biolink:Human"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1978,13 +1993,13 @@ class Plant(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Plant","biolink:Plant"]] = Field(["biolink:Plant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -1998,13 +2013,13 @@ class Invertebrate(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Invertebrate","biolink:Invertebrate"]] = Field(["biolink:Invertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2018,13 +2033,13 @@ class Vertebrate(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Vertebrate","biolink:Vertebrate"]] = Field(["biolink:Vertebrate"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2038,13 +2053,13 @@ class Fungus(CellularOrganism): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Fungus","biolink:Fungus"]] = Field(["biolink:Fungus"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2058,13 +2073,13 @@ class LifeStage(OrganismalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/LifeStage","biolink:LifeStage"]] = Field(["biolink:LifeStage"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2078,13 +2093,13 @@ class IndividualOrganism(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/IndividualOrganism","biolink:IndividualOrganism"]] = Field(["biolink:IndividualOrganism"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2098,13 +2113,13 @@ class PopulationOfIndividualOrganisms(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PopulationOfIndividualOrganisms","biolink:PopulationOfIndividualOrganisms"]] = Field(["biolink:PopulationOfIndividualOrganisms"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2118,13 +2133,13 @@ class StudyPopulation(PopulationOfIndividualOrganisms): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/StudyPopulation","biolink:StudyPopulation"]] = Field(["biolink:StudyPopulation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2138,13 +2153,13 @@ class DiseaseOrPhenotypicFeature(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeature","biolink:DiseaseOrPhenotypicFeature"]] = Field(["biolink:DiseaseOrPhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2158,13 +2173,13 @@ class Disease(DiseaseOrPhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Disease","biolink:Disease"]] = Field(["biolink:Disease"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2178,13 +2193,13 @@ class PhenotypicFeature(DiseaseOrPhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicFeature","biolink:PhenotypicFeature"]] = Field(["biolink:PhenotypicFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2198,13 +2213,13 @@ class BehavioralFeature(PhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BehavioralFeature","biolink:BehavioralFeature"]] = Field(["biolink:BehavioralFeature"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2218,13 +2233,13 @@ class AnatomicalEntity(OrganismalEntity, PhysicalEssence): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntity","biolink:AnatomicalEntity"]] = Field(["biolink:AnatomicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2238,13 +2253,13 @@ class CellularComponent(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellularComponent","biolink:CellularComponent"]] = Field(["biolink:CellularComponent"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2255,13 +2270,13 @@ class Cell(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Cell","biolink:Cell"]] = Field(["biolink:Cell"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2272,13 +2287,13 @@ class CellLine(OrganismalEntity, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLine","biolink:CellLine"]] = Field(["biolink:CellLine"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2289,13 +2304,13 @@ class GrossAnatomicalStructure(AnatomicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GrossAnatomicalStructure","biolink:GrossAnatomicalStructure"]] = Field(["biolink:GrossAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -2318,12 +2333,12 @@ class RegulatoryRegion(ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, Biologi in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RegulatoryRegion","biolink:RegulatoryRegion"]] = Field(["biolink:RegulatoryRegion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2339,12 +2354,12 @@ class AccessibleDnaRegion(RegulatoryRegion, ChemicalEntityOrGeneOrGeneProduct, G in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AccessibleDnaRegion","biolink:AccessibleDnaRegion"]] = Field(["biolink:AccessibleDnaRegion"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2360,12 +2375,12 @@ class TranscriptionFactorBindingSite(RegulatoryRegion, ChemicalEntityOrGeneOrGen in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TranscriptionFactorBindingSite","biolink:TranscriptionFactorBindingSite"]] = Field(["biolink:TranscriptionFactorBindingSite"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2389,13 +2404,13 @@ class ChemicalEntity(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneO is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntity","biolink:ChemicalEntity"]] = Field(["biolink:ChemicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2413,13 +2428,13 @@ class MolecularEntity(ChemicalEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularEntity","biolink:MolecularEntity"]] = Field(["biolink:MolecularEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2437,13 +2452,13 @@ class SmallMolecule(MolecularEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SmallMolecule","biolink:SmallMolecule"]] = Field(["biolink:SmallMolecule"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2464,13 +2479,13 @@ class ChemicalMixture(ChemicalEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalMixture","biolink:ChemicalMixture"]] = Field(["biolink:ChemicalMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2492,12 +2507,12 @@ class NucleicAcidEntity(MolecularEntity, GenomicEntity, ThingWithTaxon, Physical is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleicAcidEntity","biolink:NucleicAcidEntity"]] = Field(["biolink:NucleicAcidEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2518,13 +2533,13 @@ class MolecularMixture(ChemicalMixture): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularMixture","biolink:MolecularMixture"]] = Field(["biolink:MolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2545,13 +2560,13 @@ class ComplexMolecularMixture(ChemicalMixture): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ComplexMolecularMixture","biolink:ComplexMolecularMixture"]] = Field(["biolink:ComplexMolecularMixture"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2572,13 +2587,13 @@ class ProcessedMaterial(ChemicalMixture): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProcessedMaterial","biolink:ProcessedMaterial"]] = Field(["biolink:ProcessedMaterial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2600,12 +2615,12 @@ class Drug(MolecularMixture, ChemicalOrDrugOrTreatment, OntologyClass): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Drug","biolink:Drug"]] = Field(["biolink:Drug"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2619,13 +2634,13 @@ class EnvironmentalFoodContaminant(ChemicalEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalFoodContaminant","biolink:EnvironmentalFoodContaminant"]] = Field(["biolink:EnvironmentalFoodContaminant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2639,13 +2654,13 @@ class FoodAdditive(ChemicalEntity): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/FoodAdditive","biolink:FoodAdditive"]] = Field(["biolink:FoodAdditive"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2666,13 +2681,13 @@ class Food(ChemicalMixture): is_toxic: Optional[bool] = Field(None) has_chemical_role: Optional[List[str]] = Field(None, description="""A role is particular behaviour which a chemical entity may exhibit.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Food","biolink:Food"]] = Field(["biolink:Food"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2698,17 +2713,17 @@ class Gene(GeneOrGeneProduct, ChemicalEntityOrGeneOrGeneProduct, GenomicEntity, A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions. """ symbol: Optional[str] = Field(None, description="""Symbol for a particular thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") has_biological_sequence: Optional[str] = Field(None, description="""connects a genomic feature to its sequence""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Gene","biolink:Gene"]] = Field(["biolink:Gene"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2719,8 +2734,8 @@ class GeneProductMixin(GeneOrGeneProduct): """ The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules. """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") @@ -2728,8 +2743,8 @@ class GeneProductIsoformMixin(GeneProductMixin): """ This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms. """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") @@ -2741,13 +2756,13 @@ class MacromolecularComplex(MacromolecularMachineMixin, BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularComplex","biolink:MacromolecularComplex"]] = Field(["biolink:MacromolecularComplex"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -2761,13 +2776,13 @@ class NucleosomeModification(GeneProductIsoformMixin, EpigenomicEntity, GenomicE in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleosomeModification","biolink:NucleosomeModification"]] = Field(["biolink:NucleosomeModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2783,12 +2798,12 @@ class Genome(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Genome","biolink:Genome"]] = Field(["biolink:Genome"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2802,13 +2817,13 @@ class Exon(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Exon","biolink:Exon"]] = Field(["biolink:Exon"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2822,13 +2837,13 @@ class Transcript(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Transcript","biolink:Transcript"]] = Field(["biolink:Transcript"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2840,13 +2855,13 @@ class CodingSequence(GenomicEntity, BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CodingSequence","biolink:CodingSequence"]] = Field(["biolink:CodingSequence"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2860,13 +2875,13 @@ class Polypeptide(ChemicalEntityOrProteinOrPolypeptide, ChemicalEntityOrGeneOrGe in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Polypeptide","biolink:Polypeptide"]] = Field(["biolink:Polypeptide"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2877,8 +2892,8 @@ class Protein(Polypeptide, GeneProductMixin): """ A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -2886,7 +2901,7 @@ class Protein(Polypeptide, GeneProductMixin): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Protein","biolink:Protein"]] = Field(["biolink:Protein"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2897,8 +2912,8 @@ class ProteinIsoform(Protein, GeneProductIsoformMixin): """ Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/ """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -2906,7 +2921,7 @@ class ProteinIsoform(Protein, GeneProductIsoformMixin): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinIsoform","biolink:ProteinIsoform"]] = Field(["biolink:ProteinIsoform"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2920,13 +2935,13 @@ class PosttranslationalModification(GeneProductIsoformMixin, BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PosttranslationalModification","biolink:PosttranslationalModification"]] = Field(["biolink:PosttranslationalModification"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2940,13 +2955,13 @@ class NucleicAcidSequenceMotif(BiologicalEntity): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NucleicAcidSequenceMotif","biolink:NucleicAcidSequenceMotif"]] = Field(["biolink:NucleicAcidSequenceMotif"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2954,8 +2969,8 @@ class NucleicAcidSequenceMotif(BiologicalEntity): class RNAProduct(Transcript, GeneProductMixin): - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -2963,7 +2978,7 @@ class RNAProduct(Transcript, GeneProductMixin): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RNAProduct","biolink:RNAProduct"]] = Field(["biolink:RNAProduct"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2974,8 +2989,8 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): """ Represents a protein that is a specific isoform of the canonical or reference RNA """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -2983,7 +2998,7 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/RNAProductIsoform","biolink:RNAProductIsoform"]] = Field(["biolink:RNAProductIsoform"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -2991,8 +3006,8 @@ class RNAProductIsoform(RNAProduct, GeneProductIsoformMixin): class NoncodingRNAProduct(RNAProduct): - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -3000,7 +3015,7 @@ class NoncodingRNAProduct(RNAProduct): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NoncodingRNAProduct","biolink:NoncodingRNAProduct"]] = Field(["biolink:NoncodingRNAProduct"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3008,8 +3023,8 @@ class NoncodingRNAProduct(RNAProduct): class MicroRNA(NoncodingRNAProduct): - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -3017,7 +3032,7 @@ class MicroRNA(NoncodingRNAProduct): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MicroRNA","biolink:MicroRNA"]] = Field(["biolink:MicroRNA"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3028,8 +3043,8 @@ class SiRNA(NoncodingRNAProduct): """ A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. """ - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") @@ -3037,7 +3052,7 @@ class SiRNA(NoncodingRNAProduct): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SiRNA","biolink:SiRNA"]] = Field(["biolink:SiRNA"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3059,13 +3074,13 @@ class ProteinDomain(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinDomain","biolink:ProteinDomain"]] = Field(["biolink:ProteinDomain"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3077,13 +3092,13 @@ class ProteinFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biolog in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProteinFamily","biolink:ProteinFamily"]] = Field(["biolink:ProteinFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3098,13 +3113,13 @@ class GeneFamily(GeneGroupingMixin, ChemicalEntityOrGeneOrGeneProduct, Biologica in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneFamily","biolink:GeneFamily"]] = Field(["biolink:GeneFamily"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3119,11 +3134,11 @@ class Zygosity(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/Zygosity","biolink:Zygosity"]] = Field(["biolink:Zygosity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3139,12 +3154,12 @@ class Genotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Genotype","biolink:Genotype"]] = Field(["biolink:Genotype"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3160,12 +3175,12 @@ class Haplotype(GenomicEntity, BiologicalEntity, PhysicalEssence, OntologyClass) in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Haplotype","biolink:Haplotype"]] = Field(["biolink:Haplotype"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3182,12 +3197,12 @@ class SequenceVariant(GenomicEntity, BiologicalEntity, PhysicalEssence, Ontology in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceVariant","biolink:SequenceVariant"]] = Field(["biolink:SequenceVariant"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3204,12 +3219,12 @@ class Snv(SequenceVariant): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Snv","biolink:Snv"]] = Field(["biolink:Snv"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3225,12 +3240,12 @@ class ReagentTargetedGene(GenomicEntity, BiologicalEntity, PhysicalEssence, Onto in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ReagentTargetedGene","biolink:ReagentTargetedGene"]] = Field(["biolink:ReagentTargetedGene"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3248,11 +3263,11 @@ class ClinicalAttribute(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalAttribute","biolink:ClinicalAttribute"]] = Field(["biolink:ClinicalAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3269,11 +3284,11 @@ class ClinicalMeasurement(ClinicalAttribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalMeasurement","biolink:ClinicalMeasurement"]] = Field(["biolink:ClinicalMeasurement"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3290,11 +3305,11 @@ class ClinicalModifier(ClinicalAttribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalModifier","biolink:ClinicalModifier"]] = Field(["biolink:ClinicalModifier"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3311,11 +3326,11 @@ class ClinicalCourse(ClinicalAttribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalCourse","biolink:ClinicalCourse"]] = Field(["biolink:ClinicalCourse"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3332,11 +3347,11 @@ class Onset(ClinicalCourse): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/Onset","biolink:Onset"]] = Field(["biolink:Onset"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3347,13 +3362,13 @@ class ClinicalEntity(NamedThing): Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities """ provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalEntity","biolink:ClinicalEntity"]] = Field(["biolink:ClinicalEntity"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3362,13 +3377,13 @@ class ClinicalEntity(NamedThing): class ClinicalTrial(ClinicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalTrial","biolink:ClinicalTrial"]] = Field(["biolink:ClinicalTrial"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3377,13 +3392,13 @@ class ClinicalTrial(ClinicalEntity): class ClinicalIntervention(ClinicalEntity): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalIntervention","biolink:ClinicalIntervention"]] = Field(["biolink:ClinicalIntervention"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3397,13 +3412,13 @@ class ClinicalFinding(PhenotypicFeature): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ClinicalFinding","biolink:ClinicalFinding"]] = Field(["biolink:ClinicalFinding"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3412,13 +3427,13 @@ class ClinicalFinding(PhenotypicFeature): class Hospitalization(ClinicalIntervention): provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Hospitalization","biolink:Hospitalization"]] = Field(["biolink:Hospitalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3436,11 +3451,11 @@ class SocioeconomicAttribute(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicAttribute","biolink:SocioeconomicAttribute"]] = Field(["biolink:SocioeconomicAttribute"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3453,13 +3468,13 @@ class Case(IndividualOrganism, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Case","biolink:Case"]] = Field(["biolink:Case"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3473,13 +3488,13 @@ class Cohort(StudyPopulation, SubjectOfInvestigation): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Cohort","biolink:Cohort"]] = Field(["biolink:Cohort"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3510,11 +3525,11 @@ class GenomicBackgroundExposure(ExposureEvent, GeneGroupingMixin, GenomicEntity, has_qualitative_value: Optional[str] = Field(None, description="""connects an attribute to a value""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/GenomicBackgroundExposure","biolink:GenomicBackgroundExposure"]] = Field(["biolink:GenomicBackgroundExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3538,12 +3553,12 @@ class PathologicalProcess(PathologicalEntityMixin, BiologicalProcess): in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalProcess","biolink:PathologicalProcess"]] = Field(["biolink:PathologicalProcess"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3562,11 +3577,11 @@ class PathologicalProcessExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalProcessExposure","biolink:PathologicalProcessExposure"]] = Field(["biolink:PathologicalProcessExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3579,13 +3594,13 @@ class PathologicalAnatomicalStructure(PathologicalEntityMixin, AnatomicalEntity) in_taxon: Optional[List[str]] = Field(None, description="""connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'""") in_taxon_label: Optional[str] = Field(None, description="""The human readable scientific name for the taxon of the entity.""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalStructure","biolink:PathologicalAnatomicalStructure"]] = Field(["biolink:PathologicalAnatomicalStructure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""may often be an organism attribute""") @@ -3604,11 +3619,11 @@ class PathologicalAnatomicalExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/PathologicalAnatomicalExposure","biolink:PathologicalAnatomicalExposure"]] = Field(["biolink:PathologicalAnatomicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3626,11 +3641,11 @@ class DiseaseOrPhenotypicFeatureExposure(PathologicalEntityMixin, ExposureEvent, iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureExposure","biolink:DiseaseOrPhenotypicFeatureExposure"]] = Field(["biolink:DiseaseOrPhenotypicFeatureExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3648,11 +3663,11 @@ class ChemicalExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalExposure","biolink:ChemicalExposure"]] = Field(["biolink:ChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3669,11 +3684,11 @@ class ComplexChemicalExposure(Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/ComplexChemicalExposure","biolink:ComplexChemicalExposure"]] = Field(["biolink:ComplexChemicalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3691,11 +3706,11 @@ class DrugExposure(ChemicalExposure, ExposureEvent): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/DrugExposure","biolink:DrugExposure"]] = Field(["biolink:DrugExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3714,11 +3729,11 @@ class DrugToGeneInteractionExposure(DrugExposure, GeneGroupingMixin): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/DrugToGeneInteractionExposure","biolink:DrugToGeneInteractionExposure"]] = Field(["biolink:DrugToGeneInteractionExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3733,13 +3748,13 @@ class Treatment(ExposureEvent, NamedThing, ChemicalOrDrugOrTreatment): has_procedure: Optional[List[str]] = Field(None, description="""connects an entity to one or more (medical) procedures""") timepoint: Optional[str] = Field(None, description="""a point in time""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Treatment","biolink:Treatment"]] = Field(["biolink:Treatment"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3758,11 +3773,11 @@ class BioticExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/BioticExposure","biolink:BioticExposure"]] = Field(["biolink:BioticExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3780,11 +3795,11 @@ class EnvironmentalExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/EnvironmentalExposure","biolink:EnvironmentalExposure"]] = Field(["biolink:EnvironmentalExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3802,11 +3817,11 @@ class GeographicExposure(EnvironmentalExposure, ExposureEvent): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/GeographicExposure","biolink:GeographicExposure"]] = Field(["biolink:GeographicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3824,11 +3839,11 @@ class BehavioralExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/BehavioralExposure","biolink:BehavioralExposure"]] = Field(["biolink:BehavioralExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3846,11 +3861,11 @@ class SocioeconomicExposure(ExposureEvent, Attribute): iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") provided_by: Optional[List[str]] = Field(None, description="""The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.""") - xref: Optional[List[str]] = Field(default_factory=list, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") + xref: Optional[List[str]] = Field(None, description="""A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.""") full_name: Optional[str] = Field(None, description="""a long-form human readable name for a thing""") - synonym: Optional[List[str]] = Field(default_factory=list, description="""Alternate human-readable names for a thing""") + synonym: Optional[List[str]] = Field(None, description="""Alternate human-readable names for a thing""") category: List[Literal["https://w3id.org/biolink/vocab/SocioeconomicExposure","biolink:SocioeconomicExposure"]] = Field(["biolink:SocioeconomicExposure"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list) + type: Optional[List[str]] = Field(None) description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: List[str] = Field(..., description="""connects any entity to an attribute""") deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") @@ -3928,8 +3943,8 @@ class Association(Entity): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -3957,7 +3972,7 @@ class Association(Entity): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/Association","biolink:Association"]] = Field(["biolink:Association"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -3970,8 +3985,8 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -3999,7 +4014,7 @@ class ChemicalEntityAssessesNamedThingAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntityAssessesNamedThingAssociation","biolink:ChemicalEntityAssessesNamedThingAssociation"]] = Field(["biolink:ChemicalEntityAssessesNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4015,8 +4030,8 @@ class ContributorAssociation(Association): object: str = Field(..., description="""agent helping to realise the given entity (e.g. such as a publication)""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4044,7 +4059,7 @@ class ContributorAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ContributorAssociation","biolink:ContributorAssociation"]] = Field(["biolink:ContributorAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4060,8 +4075,8 @@ class GenotypeToGenotypePartAssociation(Association): object: str = Field(..., description="""child genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4089,7 +4104,7 @@ class GenotypeToGenotypePartAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToGenotypePartAssociation","biolink:GenotypeToGenotypePartAssociation"]] = Field(["biolink:GenotypeToGenotypePartAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4105,8 +4120,8 @@ class GenotypeToGeneAssociation(Association): object: str = Field(..., description="""gene implicated in genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4134,7 +4149,7 @@ class GenotypeToGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToGeneAssociation","biolink:GenotypeToGeneAssociation"]] = Field(["biolink:GenotypeToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4150,8 +4165,8 @@ class GenotypeToVariantAssociation(Association): object: str = Field(..., description="""gene implicated in genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4179,7 +4194,7 @@ class GenotypeToVariantAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToVariantAssociation","biolink:GenotypeToVariantAssociation"]] = Field(["biolink:GenotypeToVariantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4195,8 +4210,8 @@ class GeneToGeneAssociation(Association): object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4224,7 +4239,7 @@ class GeneToGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneAssociation","biolink:GeneToGeneAssociation"]] = Field(["biolink:GeneToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4240,8 +4255,8 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4269,7 +4284,7 @@ class GeneToGeneHomologyAssociation(GeneToGeneAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneHomologyAssociation","biolink:GeneToGeneHomologyAssociation"]] = Field(["biolink:GeneToGeneHomologyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4285,8 +4300,8 @@ class GeneToGeneFamilyAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4314,7 +4329,7 @@ class GeneToGeneFamilyAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneFamilyAssociation","biolink:GeneToGeneFamilyAssociation"]] = Field(["biolink:GeneToGeneFamilyAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4344,8 +4359,8 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4373,7 +4388,7 @@ class GeneToGeneCoexpressionAssociation(GeneExpressionMixin, GeneToGeneAssociati id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneCoexpressionAssociation","biolink:GeneToGeneCoexpressionAssociation"]] = Field(["biolink:GeneToGeneCoexpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4389,8 +4404,8 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4418,7 +4433,7 @@ class PairwiseGeneToGeneInteraction(GeneToGeneAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PairwiseGeneToGeneInteraction","biolink:PairwiseGeneToGeneInteraction"]] = Field(["biolink:PairwiseGeneToGeneInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4435,8 +4450,8 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): object: str = Field(..., description="""the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4464,7 +4479,7 @@ class PairwiseMolecularInteraction(PairwiseGeneToGeneInteraction): id: str = Field(..., description="""identifier for the interaction. This may come from an interaction database such as IMEX.""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PairwiseMolecularInteraction","biolink:PairwiseMolecularInteraction"]] = Field(["biolink:PairwiseMolecularInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4525,8 +4540,8 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio object: str = Field(..., description="""the chemical element that is the target of the statement""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4554,7 +4569,7 @@ class ChemicalToChemicalAssociation(ChemicalToEntityAssociationMixin, Associatio id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToChemicalAssociation","biolink:ChemicalToChemicalAssociation"]] = Field(["biolink:ChemicalToChemicalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4570,8 +4585,8 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): object: str = Field(..., description="""the chemical element that is the target of the statement""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4599,7 +4614,7 @@ class ReactionToParticipantAssociation(ChemicalToChemicalAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ReactionToParticipantAssociation","biolink:ReactionToParticipantAssociation"]] = Field(["biolink:ReactionToParticipantAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4615,8 +4630,8 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): object: str = Field(..., description="""the chemical element that is the target of the statement""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4644,7 +4659,7 @@ class ReactionToCatalystAssociation(ReactionToParticipantAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ReactionToCatalystAssociation","biolink:ReactionToCatalystAssociation"]] = Field(["biolink:ReactionToCatalystAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4661,8 +4676,8 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): object: str = Field(..., description="""the downstream chemical entity""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4690,7 +4705,7 @@ class ChemicalToChemicalDerivationAssociation(ChemicalToChemicalAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToChemicalDerivationAssociation","biolink:ChemicalToChemicalDerivationAssociation"]] = Field(["biolink:ChemicalToChemicalDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4706,8 +4721,8 @@ class MolecularActivityToPathwayAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4735,7 +4750,7 @@ class MolecularActivityToPathwayAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToPathwayAssociation","biolink:MolecularActivityToPathwayAssociation"]] = Field(["biolink:MolecularActivityToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4751,8 +4766,8 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association object: str = Field(..., description="""the pathway that is affected by the chemical""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4780,7 +4795,7 @@ class ChemicalToPathwayAssociation(ChemicalToEntityAssociationMixin, Association id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToPathwayAssociation","biolink:ChemicalToPathwayAssociation"]] = Field(["biolink:ChemicalToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4798,8 +4813,8 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): population_context_qualifier: Optional[str] = Field(None, description="""a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4827,7 +4842,7 @@ class NamedThingAssociatedWithLikelihoodOfNamedThingAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/NamedThingAssociatedWithLikelihoodOfNamedThingAssociation","biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"]] = Field(["biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4851,8 +4866,8 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4880,7 +4895,7 @@ class ChemicalGeneInteractionAssociation(ChemicalToEntityAssociationMixin, Assoc id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalGeneInteractionAssociation","biolink:ChemicalGeneInteractionAssociation"]] = Field(["biolink:ChemicalGeneInteractionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4900,8 +4915,8 @@ class GeneRegulatesGeneAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4929,7 +4944,7 @@ class GeneRegulatesGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneRegulatesGeneAssociation","biolink:GeneRegulatesGeneAssociation"]] = Field(["biolink:GeneRegulatesGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -4945,8 +4960,8 @@ class ProcessRegulatesProcessAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -4974,7 +4989,7 @@ class ProcessRegulatesProcessAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ProcessRegulatesProcessAssociation","biolink:ProcessRegulatesProcessAssociation"]] = Field(["biolink:ProcessRegulatesProcessAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5005,8 +5020,8 @@ class ChemicalAffectsGeneAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5034,7 +5049,7 @@ class ChemicalAffectsGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalAffectsGeneAssociation","biolink:ChemicalAffectsGeneAssociation"]] = Field(["biolink:ChemicalAffectsGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5066,8 +5081,8 @@ class GeneAffectsChemicalAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5095,7 +5110,7 @@ class GeneAffectsChemicalAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneAffectsChemicalAssociation","biolink:GeneAffectsChemicalAssociation"]] = Field(["biolink:GeneAffectsChemicalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5111,8 +5126,8 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): object: str = Field(..., description="""the gene or gene product that is affected by the drug""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5140,7 +5155,7 @@ class DrugToGeneAssociation(DrugToEntityAssociationMixin, Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DrugToGeneAssociation","biolink:DrugToGeneAssociation"]] = Field(["biolink:DrugToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5165,8 +5180,8 @@ class MaterialSampleDerivationAssociation(Association): object: str = Field(..., description="""the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5194,7 +5209,7 @@ class MaterialSampleDerivationAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSampleDerivationAssociation","biolink:MaterialSampleDerivationAssociation"]] = Field(["biolink:MaterialSampleDerivationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5225,8 +5240,8 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5254,7 +5269,7 @@ class DiseaseToExposureEventAssociation(EntityToExposureEventAssociationMixin, D id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseToExposureEventAssociation","biolink:DiseaseToExposureEventAssociation"]] = Field(["biolink:DiseaseToExposureEventAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5281,8 +5296,8 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5310,7 +5325,7 @@ class ExposureEventToOutcomeAssociation(EntityToOutcomeAssociationMixin, Associa id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ExposureEventToOutcomeAssociation","biolink:ExposureEventToOutcomeAssociation"]] = Field(["biolink:ExposureEventToOutcomeAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5401,8 +5416,8 @@ class PhenotypicFeatureToPhenotypicFeatureAssociation(PhenotypicFeatureToEntityA object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5430,7 +5445,7 @@ class PhenotypicFeatureToPhenotypicFeatureAssociation(PhenotypicFeatureToEntityA id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicFeatureToPhenotypicFeatureAssociation","biolink:PhenotypicFeatureToPhenotypicFeatureAssociation"]] = Field(["biolink:PhenotypicFeatureToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5456,8 +5471,8 @@ class InformationContentEntityToNamedThingAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5485,7 +5500,7 @@ class InformationContentEntityToNamedThingAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/InformationContentEntityToNamedThingAssociation","biolink:InformationContentEntityToNamedThingAssociation"]] = Field(["biolink:InformationContentEntityToNamedThingAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5522,8 +5537,8 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature object: str = Field(..., description="""anatomical entity in which the disease or feature is found.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5551,7 +5566,7 @@ class DiseaseOrPhenotypicFeatureToLocationAssociation(DiseaseOrPhenotypicFeature id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToLocationAssociation","biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"]] = Field(["biolink:DiseaseOrPhenotypicFeatureToLocationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5567,8 +5582,8 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty object: str = Field(..., description="""genetic inheritance associated with the specified disease or phenotypic feature.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5596,7 +5611,7 @@ class DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation(DiseaseOrPhenoty id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation","biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"]] = Field(["biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5618,8 +5633,8 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5647,7 +5662,7 @@ class CellLineToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLineToDiseaseOrPhenotypicFeatureAssociation","biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5663,8 +5678,8 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi object: str = Field(..., description="""the disease or phenotype that is affected by the chemical""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5692,7 +5707,7 @@ class ChemicalToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhenotypi id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalToDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5709,8 +5724,8 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5738,7 +5753,7 @@ class ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation(EntityToD id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5755,8 +5770,8 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C FDA_adverse_event_level: Optional[FDAIDAAdverseEventEnum] = Field(None) negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5784,7 +5799,7 @@ class ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation(C id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation","biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5800,8 +5815,8 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe object: str = Field(..., description="""disease or phenotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5829,7 +5844,7 @@ class MaterialSampleToDiseaseOrPhenotypicFeatureAssociation(EntityToDiseaseOrPhe id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MaterialSampleToDiseaseOrPhenotypicFeatureAssociation","biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5852,8 +5867,8 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5881,7 +5896,7 @@ class GenotypeToPhenotypicFeatureAssociation(GenotypeToEntityAssociationMixin, E id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToPhenotypicFeatureAssociation","biolink:GenotypeToPhenotypicFeatureAssociation"]] = Field(["biolink:GenotypeToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5908,8 +5923,8 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5937,7 +5952,7 @@ class ExposureEventToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssoc id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ExposureEventToPhenotypicFeatureAssociation","biolink:ExposureEventToPhenotypicFeatureAssociation"]] = Field(["biolink:ExposureEventToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -5969,8 +5984,8 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -5998,7 +6013,7 @@ class DiseaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociation id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DiseaseToPhenotypicFeatureAssociation","biolink:DiseaseToPhenotypicFeatureAssociation"]] = Field(["biolink:DiseaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6021,8 +6036,8 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6050,7 +6065,7 @@ class CaseToPhenotypicFeatureAssociation(EntityToPhenotypicFeatureAssociationMix id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CaseToPhenotypicFeatureAssociation","biolink:CaseToPhenotypicFeatureAssociation"]] = Field(["biolink:CaseToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6077,8 +6092,8 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6106,7 +6121,7 @@ class BehaviorToBehavioralFeatureAssociation(EntityToPhenotypicFeatureAssociatio id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/BehaviorToBehavioralFeatureAssociation","biolink:BehaviorToBehavioralFeatureAssociation"]] = Field(["biolink:BehaviorToBehavioralFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6138,8 +6153,8 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): object: str = Field(..., description="""the pathway that includes or is affected by the gene or gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6167,7 +6182,7 @@ class GeneToPathwayAssociation(GeneToEntityAssociationMixin, Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToPathwayAssociation","biolink:GeneToPathwayAssociation"]] = Field(["biolink:GeneToPathwayAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6189,8 +6204,8 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6218,7 +6233,7 @@ class GeneToDiseaseOrPhenotypicFeatureAssociation(GeneToEntityAssociationMixin, id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToDiseaseOrPhenotypicFeatureAssociation","biolink:GeneToDiseaseOrPhenotypicFeatureAssociation"]] = Field(["biolink:GeneToDiseaseOrPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6242,8 +6257,8 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia object_direction_qualifier: Optional[DirectionQualifierEnum] = Field(None, description="""Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement).""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6271,7 +6286,7 @@ class GeneToPhenotypicFeatureAssociation(GeneToDiseaseOrPhenotypicFeatureAssocia id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToPhenotypicFeatureAssociation","biolink:GeneToPhenotypicFeatureAssociation"]] = Field(["biolink:GeneToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6295,8 +6310,8 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, Gene sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6324,7 +6339,7 @@ class GeneToDiseaseAssociation(GeneToDiseaseOrPhenotypicFeatureAssociation, Gene id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToDiseaseAssociation","biolink:GeneToDiseaseAssociation"]] = Field(["biolink:GeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6348,8 +6363,8 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssoc sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6377,7 +6392,7 @@ class CausalGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAssoc id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CausalGeneToDiseaseAssociation","biolink:CausalGeneToDiseaseAssociation"]] = Field(["biolink:CausalGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6401,8 +6416,8 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityA sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6430,7 +6445,7 @@ class CorrelatedGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityA id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CorrelatedGeneToDiseaseAssociation","biolink:CorrelatedGeneToDiseaseAssociation"]] = Field(["biolink:CorrelatedGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6454,8 +6469,8 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[DruggableGeneCategoryEnum]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6483,7 +6498,7 @@ class DruggableGeneToDiseaseAssociation(GeneToDiseaseAssociation, GeneToEntityAs id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/DruggableGeneToDiseaseAssociation","biolink:DruggableGeneToDiseaseAssociation"]] = Field(["biolink:DruggableGeneToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6505,8 +6520,8 @@ class PhenotypicFeatureToDiseaseAssociation(EntityToDiseaseAssociationMixin, Phe object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6534,7 +6549,7 @@ class PhenotypicFeatureToDiseaseAssociation(EntityToDiseaseAssociationMixin, Phe id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PhenotypicFeatureToDiseaseAssociation","biolink:PhenotypicFeatureToDiseaseAssociation"]] = Field(["biolink:PhenotypicFeatureToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6560,8 +6575,8 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6589,7 +6604,7 @@ class VariantToGeneAssociation(VariantToEntityAssociationMixin, Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToGeneAssociation","biolink:VariantToGeneAssociation"]] = Field(["biolink:VariantToGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6609,8 +6624,8 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6638,7 +6653,7 @@ class VariantToGeneExpressionAssociation(VariantToGeneAssociation, GeneExpressio id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToGeneExpressionAssociation","biolink:VariantToGeneExpressionAssociation"]] = Field(["biolink:VariantToGeneExpressionAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6659,8 +6674,8 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ frequency_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6688,7 +6703,7 @@ class VariantToPopulationAssociation(VariantToEntityAssociationMixin, FrequencyQ id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToPopulationAssociation","biolink:VariantToPopulationAssociation"]] = Field(["biolink:VariantToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6704,8 +6719,8 @@ class PopulationToPopulationAssociation(Association): object: str = Field(..., description="""the population that form the object of the association""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6733,7 +6748,7 @@ class PopulationToPopulationAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/PopulationToPopulationAssociation","biolink:PopulationToPopulationAssociation"]] = Field(["biolink:PopulationToPopulationAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6747,8 +6762,8 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6776,7 +6791,7 @@ class VariantToPhenotypicFeatureAssociation(VariantToEntityAssociationMixin, Ent id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToPhenotypicFeatureAssociation","biolink:VariantToPhenotypicFeatureAssociation"]] = Field(["biolink:VariantToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6799,8 +6814,8 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea object: str = Field(..., description="""a disease that is associated with that variant""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6828,7 +6843,7 @@ class VariantToDiseaseAssociation(VariantToEntityAssociationMixin, EntityToDisea id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantToDiseaseAssociation","biolink:VariantToDiseaseAssociation"]] = Field(["biolink:VariantToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6847,8 +6862,8 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis object: str = Field(..., description="""a disease that is associated with that genotype""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6876,7 +6891,7 @@ class GenotypeToDiseaseAssociation(GenotypeToEntityAssociationMixin, EntityToDis id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeToDiseaseAssociation","biolink:GenotypeToDiseaseAssociation"]] = Field(["biolink:GenotypeToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6907,8 +6922,8 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6936,7 +6951,7 @@ class GeneAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, GeneToDis id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneAsAModelOfDiseaseAssociation","biolink:GeneAsAModelOfDiseaseAssociation"]] = Field(["biolink:GeneAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -6957,8 +6972,8 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -6986,7 +7001,7 @@ class VariantAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Varian id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/VariantAsAModelOfDiseaseAssociation","biolink:VariantAsAModelOfDiseaseAssociation"]] = Field(["biolink:VariantAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7005,8 +7020,8 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7034,7 +7049,7 @@ class GenotypeAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, Genot id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenotypeAsAModelOfDiseaseAssociation","biolink:GenotypeAsAModelOfDiseaseAssociation"]] = Field(["biolink:GenotypeAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7053,8 +7068,8 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7082,7 +7097,7 @@ class CellLineAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixin, CellL id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/CellLineAsAModelOfDiseaseAssociation","biolink:CellLineAsAModelOfDiseaseAssociation"]] = Field(["biolink:CellLineAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7101,8 +7116,8 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi object: str = Field(..., description="""disease""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7130,7 +7145,7 @@ class OrganismalEntityAsAModelOfDiseaseAssociation(ModelToDiseaseAssociationMixi id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismalEntityAsAModelOfDiseaseAssociation","biolink:OrganismalEntityAsAModelOfDiseaseAssociation"]] = Field(["biolink:OrganismalEntityAsAModelOfDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7149,8 +7164,8 @@ class OrganismToOrganismAssociation(Association): object: str = Field(..., description="""An association between two individual organisms.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7178,7 +7193,7 @@ class OrganismToOrganismAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismToOrganismAssociation","biolink:OrganismToOrganismAssociation"]] = Field(["biolink:OrganismToOrganismAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7191,8 +7206,8 @@ class TaxonToTaxonAssociation(Association): object: str = Field(..., description="""An association between individuals of different taxa.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7220,7 +7235,7 @@ class TaxonToTaxonAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TaxonToTaxonAssociation","biolink:TaxonToTaxonAssociation"]] = Field(["biolink:TaxonToTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7237,8 +7252,8 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation sex_qualifier: Optional[str] = Field(None, description="""a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7266,7 +7281,7 @@ class GeneHasVariantThatContributesToDiseaseAssociation(GeneToDiseaseAssociation id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneHasVariantThatContributesToDiseaseAssociation","biolink:GeneHasVariantThatContributesToDiseaseAssociation"]] = Field(["biolink:GeneHasVariantThatContributesToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7292,8 +7307,8 @@ class GeneToExpressionSiteAssociation(Association): object: str = Field(..., description="""location in which the gene is expressed""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7321,7 +7336,7 @@ class GeneToExpressionSiteAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToExpressionSiteAssociation","biolink:GeneToExpressionSiteAssociation"]] = Field(["biolink:GeneToExpressionSiteAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7337,8 +7352,8 @@ class SequenceVariantModulatesTreatmentAssociation(Association): object: str = Field(..., description="""treatment whose efficacy is modulated by the subject variant""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7366,7 +7381,7 @@ class SequenceVariantModulatesTreatmentAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceVariantModulatesTreatmentAssociation","biolink:SequenceVariantModulatesTreatmentAssociation"]] = Field(["biolink:SequenceVariantModulatesTreatmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7382,8 +7397,8 @@ class FunctionalAssociation(Association): object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7411,7 +7426,7 @@ class FunctionalAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/FunctionalAssociation","biolink:FunctionalAssociation"]] = Field(["biolink:FunctionalAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7436,8 +7451,8 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7465,7 +7480,7 @@ class MacromolecularMachineToMolecularActivityAssociation(MacromolecularMachineT id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToMolecularActivityAssociation","biolink:MacromolecularMachineToMolecularActivityAssociation"]] = Field(["biolink:MacromolecularMachineToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7481,8 +7496,8 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7510,7 +7525,7 @@ class MacromolecularMachineToBiologicalProcessAssociation(MacromolecularMachineT id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToBiologicalProcessAssociation","biolink:MacromolecularMachineToBiologicalProcessAssociation"]] = Field(["biolink:MacromolecularMachineToBiologicalProcessAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7526,8 +7541,8 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7555,7 +7570,7 @@ class MacromolecularMachineToCellularComponentAssociation(MacromolecularMachineT id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MacromolecularMachineToCellularComponentAssociation","biolink:MacromolecularMachineToCellularComponentAssociation"]] = Field(["biolink:MacromolecularMachineToCellularComponentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7571,8 +7586,8 @@ class MolecularActivityToChemicalEntityAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7600,7 +7615,7 @@ class MolecularActivityToChemicalEntityAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToChemicalEntityAssociation","biolink:MolecularActivityToChemicalEntityAssociation"]] = Field(["biolink:MolecularActivityToChemicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7616,8 +7631,8 @@ class MolecularActivityToMolecularActivityAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7645,7 +7660,7 @@ class MolecularActivityToMolecularActivityAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/MolecularActivityToMolecularActivityAssociation","biolink:MolecularActivityToMolecularActivityAssociation"]] = Field(["biolink:MolecularActivityToMolecularActivityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7658,8 +7673,8 @@ class GeneToGoTermAssociation(FunctionalAssociation): object: str = Field(..., description="""class describing the activity, process or localization of the gene product""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7687,7 +7702,7 @@ class GeneToGoTermAssociation(FunctionalAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGoTermAssociation","biolink:GeneToGoTermAssociation"]] = Field(["biolink:GeneToGoTermAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7702,8 +7717,8 @@ class EntityToDiseaseAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7731,7 +7746,7 @@ class EntityToDiseaseAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EntityToDiseaseAssociation","biolink:EntityToDiseaseAssociation"]] = Field(["biolink:EntityToDiseaseAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7746,8 +7761,8 @@ class EntityToPhenotypicFeatureAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7775,7 +7790,7 @@ class EntityToPhenotypicFeatureAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociation","biolink:EntityToPhenotypicFeatureAssociation"]] = Field(["biolink:EntityToPhenotypicFeatureAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7791,8 +7806,8 @@ class SequenceAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7820,7 +7835,7 @@ class SequenceAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceAssociation","biolink:SequenceAssociation"]] = Field(["biolink:SequenceAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7841,8 +7856,8 @@ class GenomicSequenceLocalization(SequenceAssociation): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7870,7 +7885,7 @@ class GenomicSequenceLocalization(SequenceAssociation): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GenomicSequenceLocalization","biolink:GenomicSequenceLocalization"]] = Field(["biolink:GenomicSequenceLocalization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7886,8 +7901,8 @@ class SequenceFeatureRelationship(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7915,7 +7930,7 @@ class SequenceFeatureRelationship(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/SequenceFeatureRelationship","biolink:SequenceFeatureRelationship"]] = Field(["biolink:SequenceFeatureRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7931,8 +7946,8 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -7960,7 +7975,7 @@ class TranscriptToGeneRelationship(SequenceFeatureRelationship): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/TranscriptToGeneRelationship","biolink:TranscriptToGeneRelationship"]] = Field(["biolink:TranscriptToGeneRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -7976,8 +7991,8 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8005,7 +8020,7 @@ class GeneToGeneProductRelationship(SequenceFeatureRelationship): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/GeneToGeneProductRelationship","biolink:GeneToGeneProductRelationship"]] = Field(["biolink:GeneToGeneProductRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8021,8 +8036,8 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8050,7 +8065,7 @@ class ExonToTranscriptRelationship(SequenceFeatureRelationship): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ExonToTranscriptRelationship","biolink:ExonToTranscriptRelationship"]] = Field(["biolink:ExonToTranscriptRelationship"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8067,8 +8082,8 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8096,7 +8111,7 @@ class ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation","biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"]] = Field(["biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8109,8 +8124,8 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8138,7 +8153,7 @@ class AnatomicalEntityToAnatomicalEntityAssociation(Association): id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityAssociation","biolink:AnatomicalEntityToAnatomicalEntityAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8154,8 +8169,8 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat object: str = Field(..., description="""the whole""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8183,7 +8198,7 @@ class AnatomicalEntityToAnatomicalEntityPartOfAssociation(AnatomicalEntityToAnat id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityPartOfAssociation","biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8199,8 +8214,8 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA object: str = Field(..., description="""the structure at an earlier time""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8228,7 +8243,7 @@ class AnatomicalEntityToAnatomicalEntityOntogenicAssociation(AnatomicalEntityToA id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/AnatomicalEntityToAnatomicalEntityOntogenicAssociation","biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation"]] = Field(["biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8253,8 +8268,8 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, object: str = Field(..., description="""connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8282,7 +8297,7 @@ class OrganismTaxonToOrganismTaxonAssociation(OrganismTaxonToEntityAssociation, id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonAssociation","biolink:OrganismTaxonToOrganismTaxonAssociation"]] = Field(["biolink:OrganismTaxonToOrganismTaxonAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8298,8 +8313,8 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss object: str = Field(..., description="""the more general taxon""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8327,7 +8342,7 @@ class OrganismTaxonToOrganismTaxonSpecialization(OrganismTaxonToOrganismTaxonAss id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonSpecialization","biolink:OrganismTaxonToOrganismTaxonSpecialization"]] = Field(["biolink:OrganismTaxonToOrganismTaxonSpecialization"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8344,8 +8359,8 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci object: str = Field(..., description="""the taxon that is the subject of the association""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8373,7 +8388,7 @@ class OrganismTaxonToOrganismTaxonInteraction(OrganismTaxonToOrganismTaxonAssoci id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToOrganismTaxonInteraction","biolink:OrganismTaxonToOrganismTaxonInteraction"]] = Field(["biolink:OrganismTaxonToOrganismTaxonInteraction"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") description: Optional[str] = Field(None, description="""a human-readable description of an entity""") has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") @@ -8386,8 +8401,8 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As object: str = Field(..., description="""the environment in which the organism occurs""") negated: Optional[bool] = Field(None, description="""if set to true, then the association is negated i.e. is not true""") qualifier: Optional[str] = Field(None, description="""grouping slot for all qualifiers on an edge. useful for testing compliance with association classes""") - qualifiers: Optional[List[str]] = Field(default_factory=list, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") - publications: Optional[List[str]] = Field(default_factory=list, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") + qualifiers: Optional[List[str]] = Field(None, description="""connects an association to qualifiers that modify or qualify the meaning of that association""") + publications: Optional[List[str]] = Field(None, description="""One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.""") has_evidence: Optional[List[str]] = Field(None, description="""connects an association to an instance of supporting evidence""") knowledge_source: Optional[str] = Field(None, description="""An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.""") primary_knowledge_source: Optional[str] = Field(None, description="""The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources.""") @@ -8415,321 +8430,321 @@ class OrganismTaxonToEnvironmentAssociation(OrganismTaxonToEntityAssociation, As id: str = Field(..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""") iri: Optional[str] = Field(None, description="""An IRI for an entity. This is determined by the id using expansion rules.""") category: List[Literal["https://w3id.org/biolink/vocab/OrganismTaxonToEnvironmentAssociation","biolink:OrganismTaxonToEnvironmentAssociation"]] = Field(["biolink:OrganismTaxonToEnvironmentAssociation"], description="""Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}""") - type: Optional[List[str]] = Field(default_factory=list, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") - name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") - description: Optional[str] = Field(None, description="""a human-readable description of an entity""") - has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") - deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") - - -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -MappingCollection.update_forward_refs() -PredicateMapping.update_forward_refs() -OntologyClass.update_forward_refs() -Annotation.update_forward_refs() -QuantityValue.update_forward_refs() -RelationshipQuantifier.update_forward_refs() -SensitivityQuantifier.update_forward_refs() -SpecificityQuantifier.update_forward_refs() -PathognomonicityQuantifier.update_forward_refs() -FrequencyQuantifier.update_forward_refs() -ChemicalOrDrugOrTreatment.update_forward_refs() -Entity.update_forward_refs() -NamedThing.update_forward_refs() -Attribute.update_forward_refs() -ChemicalRole.update_forward_refs() -BiologicalSex.update_forward_refs() -PhenotypicSex.update_forward_refs() -GenotypicSex.update_forward_refs() -SeverityValue.update_forward_refs() -RelationshipType.update_forward_refs() -TaxonomicRank.update_forward_refs() -OrganismTaxon.update_forward_refs() -Event.update_forward_refs() -AdministrativeEntity.update_forward_refs() -Agent.update_forward_refs() -InformationContentEntity.update_forward_refs() -StudyResult.update_forward_refs() -StudyVariable.update_forward_refs() -CommonDataElement.update_forward_refs() -ConceptCountAnalysisResult.update_forward_refs() -ObservedExpectedFrequencyAnalysisResult.update_forward_refs() -RelativeFrequencyAnalysisResult.update_forward_refs() -TextMiningResult.update_forward_refs() -ChiSquaredAnalysisResult.update_forward_refs() -LogOddsAnalysisResult.update_forward_refs() -Dataset.update_forward_refs() -DatasetDistribution.update_forward_refs() -DatasetVersion.update_forward_refs() -DatasetSummary.update_forward_refs() -ConfidenceLevel.update_forward_refs() -EvidenceType.update_forward_refs() -Publication.update_forward_refs() -Book.update_forward_refs() -BookChapter.update_forward_refs() -Serial.update_forward_refs() -Article.update_forward_refs() -JournalArticle.update_forward_refs() -Patent.update_forward_refs() -WebPage.update_forward_refs() -PreprintPublication.update_forward_refs() -DrugLabel.update_forward_refs() -RetrievalSource.update_forward_refs() -PhysicalEssenceOrOccurrent.update_forward_refs() -PhysicalEssence.update_forward_refs() -PhysicalEntity.update_forward_refs() -Occurrent.update_forward_refs() -ActivityAndBehavior.update_forward_refs() -Activity.update_forward_refs() -Study.update_forward_refs() -Procedure.update_forward_refs() -Phenomenon.update_forward_refs() -Device.update_forward_refs() -DiagnosticAid.update_forward_refs() -SubjectOfInvestigation.update_forward_refs() -MaterialSample.update_forward_refs() -PlanetaryEntity.update_forward_refs() -EnvironmentalProcess.update_forward_refs() -EnvironmentalFeature.update_forward_refs() -GeographicLocation.update_forward_refs() -GeographicLocationAtTime.update_forward_refs() -ThingWithTaxon.update_forward_refs() -BiologicalEntity.update_forward_refs() -GenomicEntity.update_forward_refs() -EpigenomicEntity.update_forward_refs() -BiologicalProcessOrActivity.update_forward_refs() -MolecularActivity.update_forward_refs() -BiologicalProcess.update_forward_refs() -Pathway.update_forward_refs() -PhysiologicalProcess.update_forward_refs() -Behavior.update_forward_refs() -OrganismAttribute.update_forward_refs() -PhenotypicQuality.update_forward_refs() -GeneticInheritance.update_forward_refs() -OrganismalEntity.update_forward_refs() -Bacterium.update_forward_refs() -Virus.update_forward_refs() -CellularOrganism.update_forward_refs() -Mammal.update_forward_refs() -Human.update_forward_refs() -Plant.update_forward_refs() -Invertebrate.update_forward_refs() -Vertebrate.update_forward_refs() -Fungus.update_forward_refs() -LifeStage.update_forward_refs() -IndividualOrganism.update_forward_refs() -PopulationOfIndividualOrganisms.update_forward_refs() -StudyPopulation.update_forward_refs() -DiseaseOrPhenotypicFeature.update_forward_refs() -Disease.update_forward_refs() -PhenotypicFeature.update_forward_refs() -BehavioralFeature.update_forward_refs() -AnatomicalEntity.update_forward_refs() -CellularComponent.update_forward_refs() -Cell.update_forward_refs() -CellLine.update_forward_refs() -GrossAnatomicalStructure.update_forward_refs() -ChemicalEntityOrGeneOrGeneProduct.update_forward_refs() -RegulatoryRegion.update_forward_refs() -AccessibleDnaRegion.update_forward_refs() -TranscriptionFactorBindingSite.update_forward_refs() -ChemicalEntityOrProteinOrPolypeptide.update_forward_refs() -ChemicalEntity.update_forward_refs() -MolecularEntity.update_forward_refs() -SmallMolecule.update_forward_refs() -ChemicalMixture.update_forward_refs() -NucleicAcidEntity.update_forward_refs() -MolecularMixture.update_forward_refs() -ComplexMolecularMixture.update_forward_refs() -ProcessedMaterial.update_forward_refs() -Drug.update_forward_refs() -EnvironmentalFoodContaminant.update_forward_refs() -FoodAdditive.update_forward_refs() -Food.update_forward_refs() -MacromolecularMachineMixin.update_forward_refs() -GeneOrGeneProduct.update_forward_refs() -Gene.update_forward_refs() -GeneProductMixin.update_forward_refs() -GeneProductIsoformMixin.update_forward_refs() -MacromolecularComplex.update_forward_refs() -NucleosomeModification.update_forward_refs() -Genome.update_forward_refs() -Exon.update_forward_refs() -Transcript.update_forward_refs() -CodingSequence.update_forward_refs() -Polypeptide.update_forward_refs() -Protein.update_forward_refs() -ProteinIsoform.update_forward_refs() -PosttranslationalModification.update_forward_refs() -NucleicAcidSequenceMotif.update_forward_refs() -RNAProduct.update_forward_refs() -RNAProductIsoform.update_forward_refs() -NoncodingRNAProduct.update_forward_refs() -MicroRNA.update_forward_refs() -SiRNA.update_forward_refs() -GeneGroupingMixin.update_forward_refs() -ProteinDomain.update_forward_refs() -ProteinFamily.update_forward_refs() -GeneFamily.update_forward_refs() -Zygosity.update_forward_refs() -Genotype.update_forward_refs() -Haplotype.update_forward_refs() -SequenceVariant.update_forward_refs() -Snv.update_forward_refs() -ReagentTargetedGene.update_forward_refs() -ClinicalAttribute.update_forward_refs() -ClinicalMeasurement.update_forward_refs() -ClinicalModifier.update_forward_refs() -ClinicalCourse.update_forward_refs() -Onset.update_forward_refs() -ClinicalEntity.update_forward_refs() -ClinicalTrial.update_forward_refs() -ClinicalIntervention.update_forward_refs() -ClinicalFinding.update_forward_refs() -Hospitalization.update_forward_refs() -SocioeconomicAttribute.update_forward_refs() -Case.update_forward_refs() -Cohort.update_forward_refs() -ExposureEvent.update_forward_refs() -GenomicBackgroundExposure.update_forward_refs() -PathologicalEntityMixin.update_forward_refs() -PathologicalProcess.update_forward_refs() -PathologicalProcessExposure.update_forward_refs() -PathologicalAnatomicalStructure.update_forward_refs() -PathologicalAnatomicalExposure.update_forward_refs() -DiseaseOrPhenotypicFeatureExposure.update_forward_refs() -ChemicalExposure.update_forward_refs() -ComplexChemicalExposure.update_forward_refs() -DrugExposure.update_forward_refs() -DrugToGeneInteractionExposure.update_forward_refs() -Treatment.update_forward_refs() -BioticExposure.update_forward_refs() -EnvironmentalExposure.update_forward_refs() -GeographicExposure.update_forward_refs() -BehavioralExposure.update_forward_refs() -SocioeconomicExposure.update_forward_refs() -Outcome.update_forward_refs() -PathologicalProcessOutcome.update_forward_refs() -PathologicalAnatomicalOutcome.update_forward_refs() -DiseaseOrPhenotypicFeatureOutcome.update_forward_refs() -BehavioralOutcome.update_forward_refs() -HospitalizationOutcome.update_forward_refs() -MortalityOutcome.update_forward_refs() -EpidemiologicalOutcome.update_forward_refs() -SocioeconomicOutcome.update_forward_refs() -Association.update_forward_refs() -ChemicalEntityAssessesNamedThingAssociation.update_forward_refs() -ContributorAssociation.update_forward_refs() -GenotypeToGenotypePartAssociation.update_forward_refs() -GenotypeToGeneAssociation.update_forward_refs() -GenotypeToVariantAssociation.update_forward_refs() -GeneToGeneAssociation.update_forward_refs() -GeneToGeneHomologyAssociation.update_forward_refs() -GeneToGeneFamilyAssociation.update_forward_refs() -GeneExpressionMixin.update_forward_refs() -GeneToGeneCoexpressionAssociation.update_forward_refs() -PairwiseGeneToGeneInteraction.update_forward_refs() -PairwiseMolecularInteraction.update_forward_refs() -CellLineToEntityAssociationMixin.update_forward_refs() -ChemicalEntityToEntityAssociationMixin.update_forward_refs() -DrugToEntityAssociationMixin.update_forward_refs() -ChemicalToEntityAssociationMixin.update_forward_refs() -CaseToEntityAssociationMixin.update_forward_refs() -ChemicalToChemicalAssociation.update_forward_refs() -ReactionToParticipantAssociation.update_forward_refs() -ReactionToCatalystAssociation.update_forward_refs() -ChemicalToChemicalDerivationAssociation.update_forward_refs() -MolecularActivityToPathwayAssociation.update_forward_refs() -ChemicalToPathwayAssociation.update_forward_refs() -NamedThingAssociatedWithLikelihoodOfNamedThingAssociation.update_forward_refs() -ChemicalGeneInteractionAssociation.update_forward_refs() -GeneRegulatesGeneAssociation.update_forward_refs() -ProcessRegulatesProcessAssociation.update_forward_refs() -ChemicalAffectsGeneAssociation.update_forward_refs() -GeneAffectsChemicalAssociation.update_forward_refs() -DrugToGeneAssociation.update_forward_refs() -MaterialSampleToEntityAssociationMixin.update_forward_refs() -MaterialSampleDerivationAssociation.update_forward_refs() -DiseaseToEntityAssociationMixin.update_forward_refs() -EntityToExposureEventAssociationMixin.update_forward_refs() -DiseaseToExposureEventAssociation.update_forward_refs() -EntityToOutcomeAssociationMixin.update_forward_refs() -ExposureEventToOutcomeAssociation.update_forward_refs() -FrequencyQualifierMixin.update_forward_refs() -EntityToFeatureOrDiseaseQualifiersMixin.update_forward_refs() -FeatureOrDiseaseQualifiersToEntityMixin.update_forward_refs() -EntityToPhenotypicFeatureAssociationMixin.update_forward_refs() -PhenotypicFeatureToEntityAssociationMixin.update_forward_refs() -PhenotypicFeatureToPhenotypicFeatureAssociation.update_forward_refs() -InformationContentEntityToNamedThingAssociation.update_forward_refs() -EntityToDiseaseAssociationMixin.update_forward_refs() -DiseaseOrPhenotypicFeatureToEntityAssociationMixin.update_forward_refs() -DiseaseOrPhenotypicFeatureToLocationAssociation.update_forward_refs() -DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation.update_forward_refs() -EntityToDiseaseOrPhenotypicFeatureAssociationMixin.update_forward_refs() -CellLineToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -ChemicalToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -MaterialSampleToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -GenotypeToEntityAssociationMixin.update_forward_refs() -GenotypeToPhenotypicFeatureAssociation.update_forward_refs() -ExposureEventToPhenotypicFeatureAssociation.update_forward_refs() -DiseaseToPhenotypicFeatureAssociation.update_forward_refs() -CaseToPhenotypicFeatureAssociation.update_forward_refs() -BehaviorToBehavioralFeatureAssociation.update_forward_refs() -GeneToEntityAssociationMixin.update_forward_refs() -GeneToPathwayAssociation.update_forward_refs() -VariantToEntityAssociationMixin.update_forward_refs() -GeneToDiseaseOrPhenotypicFeatureAssociation.update_forward_refs() -GeneToPhenotypicFeatureAssociation.update_forward_refs() -GeneToDiseaseAssociation.update_forward_refs() -CausalGeneToDiseaseAssociation.update_forward_refs() -CorrelatedGeneToDiseaseAssociation.update_forward_refs() -DruggableGeneToDiseaseAssociation.update_forward_refs() -PhenotypicFeatureToDiseaseAssociation.update_forward_refs() -VariantToGeneAssociation.update_forward_refs() -VariantToGeneExpressionAssociation.update_forward_refs() -VariantToPopulationAssociation.update_forward_refs() -PopulationToPopulationAssociation.update_forward_refs() -VariantToPhenotypicFeatureAssociation.update_forward_refs() -VariantToDiseaseAssociation.update_forward_refs() -GenotypeToDiseaseAssociation.update_forward_refs() -ModelToDiseaseAssociationMixin.update_forward_refs() -GeneAsAModelOfDiseaseAssociation.update_forward_refs() -VariantAsAModelOfDiseaseAssociation.update_forward_refs() -GenotypeAsAModelOfDiseaseAssociation.update_forward_refs() -CellLineAsAModelOfDiseaseAssociation.update_forward_refs() -OrganismalEntityAsAModelOfDiseaseAssociation.update_forward_refs() -OrganismToOrganismAssociation.update_forward_refs() -TaxonToTaxonAssociation.update_forward_refs() -GeneHasVariantThatContributesToDiseaseAssociation.update_forward_refs() -GeneToExpressionSiteAssociation.update_forward_refs() -SequenceVariantModulatesTreatmentAssociation.update_forward_refs() -FunctionalAssociation.update_forward_refs() -MacromolecularMachineToEntityAssociationMixin.update_forward_refs() -MacromolecularMachineToMolecularActivityAssociation.update_forward_refs() -MacromolecularMachineToBiologicalProcessAssociation.update_forward_refs() -MacromolecularMachineToCellularComponentAssociation.update_forward_refs() -MolecularActivityToChemicalEntityAssociation.update_forward_refs() -MolecularActivityToMolecularActivityAssociation.update_forward_refs() -GeneToGoTermAssociation.update_forward_refs() -EntityToDiseaseAssociation.update_forward_refs() -EntityToPhenotypicFeatureAssociation.update_forward_refs() -SequenceAssociation.update_forward_refs() -GenomicSequenceLocalization.update_forward_refs() -SequenceFeatureRelationship.update_forward_refs() -TranscriptToGeneRelationship.update_forward_refs() -GeneToGeneProductRelationship.update_forward_refs() -ExonToTranscriptRelationship.update_forward_refs() -ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation.update_forward_refs() -AnatomicalEntityToAnatomicalEntityAssociation.update_forward_refs() -AnatomicalEntityToAnatomicalEntityPartOfAssociation.update_forward_refs() -AnatomicalEntityToAnatomicalEntityOntogenicAssociation.update_forward_refs() -OrganismTaxonToEntityAssociation.update_forward_refs() -OrganismTaxonToOrganismTaxonAssociation.update_forward_refs() -OrganismTaxonToOrganismTaxonSpecialization.update_forward_refs() -OrganismTaxonToOrganismTaxonInteraction.update_forward_refs() -OrganismTaxonToEnvironmentAssociation.update_forward_refs() + type: Optional[List[str]] = Field(None, description="""rdf:type of biolink:Association should be fixed at rdf:Statement""") + name: Optional[str] = Field(None, description="""A human-readable name for an attribute or entity.""") + description: Optional[str] = Field(None, description="""a human-readable description of an entity""") + has_attribute: Optional[List[str]] = Field(None, description="""connects any entity to an attribute""") + deprecated: Optional[bool] = Field(None, description="""A boolean flag indicating that an entity is no longer considered current or valid.""") + + +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +MappingCollection.model_rebuild() +PredicateMapping.model_rebuild() +OntologyClass.model_rebuild() +Annotation.model_rebuild() +QuantityValue.model_rebuild() +RelationshipQuantifier.model_rebuild() +SensitivityQuantifier.model_rebuild() +SpecificityQuantifier.model_rebuild() +PathognomonicityQuantifier.model_rebuild() +FrequencyQuantifier.model_rebuild() +ChemicalOrDrugOrTreatment.model_rebuild() +Entity.model_rebuild() +NamedThing.model_rebuild() +Attribute.model_rebuild() +ChemicalRole.model_rebuild() +BiologicalSex.model_rebuild() +PhenotypicSex.model_rebuild() +GenotypicSex.model_rebuild() +SeverityValue.model_rebuild() +RelationshipType.model_rebuild() +TaxonomicRank.model_rebuild() +OrganismTaxon.model_rebuild() +Event.model_rebuild() +AdministrativeEntity.model_rebuild() +Agent.model_rebuild() +InformationContentEntity.model_rebuild() +StudyResult.model_rebuild() +StudyVariable.model_rebuild() +CommonDataElement.model_rebuild() +ConceptCountAnalysisResult.model_rebuild() +ObservedExpectedFrequencyAnalysisResult.model_rebuild() +RelativeFrequencyAnalysisResult.model_rebuild() +TextMiningResult.model_rebuild() +ChiSquaredAnalysisResult.model_rebuild() +LogOddsAnalysisResult.model_rebuild() +Dataset.model_rebuild() +DatasetDistribution.model_rebuild() +DatasetVersion.model_rebuild() +DatasetSummary.model_rebuild() +ConfidenceLevel.model_rebuild() +EvidenceType.model_rebuild() +Publication.model_rebuild() +Book.model_rebuild() +BookChapter.model_rebuild() +Serial.model_rebuild() +Article.model_rebuild() +JournalArticle.model_rebuild() +Patent.model_rebuild() +WebPage.model_rebuild() +PreprintPublication.model_rebuild() +DrugLabel.model_rebuild() +RetrievalSource.model_rebuild() +PhysicalEssenceOrOccurrent.model_rebuild() +PhysicalEssence.model_rebuild() +PhysicalEntity.model_rebuild() +Occurrent.model_rebuild() +ActivityAndBehavior.model_rebuild() +Activity.model_rebuild() +Study.model_rebuild() +Procedure.model_rebuild() +Phenomenon.model_rebuild() +Device.model_rebuild() +DiagnosticAid.model_rebuild() +SubjectOfInvestigation.model_rebuild() +MaterialSample.model_rebuild() +PlanetaryEntity.model_rebuild() +EnvironmentalProcess.model_rebuild() +EnvironmentalFeature.model_rebuild() +GeographicLocation.model_rebuild() +GeographicLocationAtTime.model_rebuild() +ThingWithTaxon.model_rebuild() +BiologicalEntity.model_rebuild() +GenomicEntity.model_rebuild() +EpigenomicEntity.model_rebuild() +BiologicalProcessOrActivity.model_rebuild() +MolecularActivity.model_rebuild() +BiologicalProcess.model_rebuild() +Pathway.model_rebuild() +PhysiologicalProcess.model_rebuild() +Behavior.model_rebuild() +OrganismAttribute.model_rebuild() +PhenotypicQuality.model_rebuild() +GeneticInheritance.model_rebuild() +OrganismalEntity.model_rebuild() +Bacterium.model_rebuild() +Virus.model_rebuild() +CellularOrganism.model_rebuild() +Mammal.model_rebuild() +Human.model_rebuild() +Plant.model_rebuild() +Invertebrate.model_rebuild() +Vertebrate.model_rebuild() +Fungus.model_rebuild() +LifeStage.model_rebuild() +IndividualOrganism.model_rebuild() +PopulationOfIndividualOrganisms.model_rebuild() +StudyPopulation.model_rebuild() +DiseaseOrPhenotypicFeature.model_rebuild() +Disease.model_rebuild() +PhenotypicFeature.model_rebuild() +BehavioralFeature.model_rebuild() +AnatomicalEntity.model_rebuild() +CellularComponent.model_rebuild() +Cell.model_rebuild() +CellLine.model_rebuild() +GrossAnatomicalStructure.model_rebuild() +ChemicalEntityOrGeneOrGeneProduct.model_rebuild() +RegulatoryRegion.model_rebuild() +AccessibleDnaRegion.model_rebuild() +TranscriptionFactorBindingSite.model_rebuild() +ChemicalEntityOrProteinOrPolypeptide.model_rebuild() +ChemicalEntity.model_rebuild() +MolecularEntity.model_rebuild() +SmallMolecule.model_rebuild() +ChemicalMixture.model_rebuild() +NucleicAcidEntity.model_rebuild() +MolecularMixture.model_rebuild() +ComplexMolecularMixture.model_rebuild() +ProcessedMaterial.model_rebuild() +Drug.model_rebuild() +EnvironmentalFoodContaminant.model_rebuild() +FoodAdditive.model_rebuild() +Food.model_rebuild() +MacromolecularMachineMixin.model_rebuild() +GeneOrGeneProduct.model_rebuild() +Gene.model_rebuild() +GeneProductMixin.model_rebuild() +GeneProductIsoformMixin.model_rebuild() +MacromolecularComplex.model_rebuild() +NucleosomeModification.model_rebuild() +Genome.model_rebuild() +Exon.model_rebuild() +Transcript.model_rebuild() +CodingSequence.model_rebuild() +Polypeptide.model_rebuild() +Protein.model_rebuild() +ProteinIsoform.model_rebuild() +PosttranslationalModification.model_rebuild() +NucleicAcidSequenceMotif.model_rebuild() +RNAProduct.model_rebuild() +RNAProductIsoform.model_rebuild() +NoncodingRNAProduct.model_rebuild() +MicroRNA.model_rebuild() +SiRNA.model_rebuild() +GeneGroupingMixin.model_rebuild() +ProteinDomain.model_rebuild() +ProteinFamily.model_rebuild() +GeneFamily.model_rebuild() +Zygosity.model_rebuild() +Genotype.model_rebuild() +Haplotype.model_rebuild() +SequenceVariant.model_rebuild() +Snv.model_rebuild() +ReagentTargetedGene.model_rebuild() +ClinicalAttribute.model_rebuild() +ClinicalMeasurement.model_rebuild() +ClinicalModifier.model_rebuild() +ClinicalCourse.model_rebuild() +Onset.model_rebuild() +ClinicalEntity.model_rebuild() +ClinicalTrial.model_rebuild() +ClinicalIntervention.model_rebuild() +ClinicalFinding.model_rebuild() +Hospitalization.model_rebuild() +SocioeconomicAttribute.model_rebuild() +Case.model_rebuild() +Cohort.model_rebuild() +ExposureEvent.model_rebuild() +GenomicBackgroundExposure.model_rebuild() +PathologicalEntityMixin.model_rebuild() +PathologicalProcess.model_rebuild() +PathologicalProcessExposure.model_rebuild() +PathologicalAnatomicalStructure.model_rebuild() +PathologicalAnatomicalExposure.model_rebuild() +DiseaseOrPhenotypicFeatureExposure.model_rebuild() +ChemicalExposure.model_rebuild() +ComplexChemicalExposure.model_rebuild() +DrugExposure.model_rebuild() +DrugToGeneInteractionExposure.model_rebuild() +Treatment.model_rebuild() +BioticExposure.model_rebuild() +EnvironmentalExposure.model_rebuild() +GeographicExposure.model_rebuild() +BehavioralExposure.model_rebuild() +SocioeconomicExposure.model_rebuild() +Outcome.model_rebuild() +PathologicalProcessOutcome.model_rebuild() +PathologicalAnatomicalOutcome.model_rebuild() +DiseaseOrPhenotypicFeatureOutcome.model_rebuild() +BehavioralOutcome.model_rebuild() +HospitalizationOutcome.model_rebuild() +MortalityOutcome.model_rebuild() +EpidemiologicalOutcome.model_rebuild() +SocioeconomicOutcome.model_rebuild() +Association.model_rebuild() +ChemicalEntityAssessesNamedThingAssociation.model_rebuild() +ContributorAssociation.model_rebuild() +GenotypeToGenotypePartAssociation.model_rebuild() +GenotypeToGeneAssociation.model_rebuild() +GenotypeToVariantAssociation.model_rebuild() +GeneToGeneAssociation.model_rebuild() +GeneToGeneHomologyAssociation.model_rebuild() +GeneToGeneFamilyAssociation.model_rebuild() +GeneExpressionMixin.model_rebuild() +GeneToGeneCoexpressionAssociation.model_rebuild() +PairwiseGeneToGeneInteraction.model_rebuild() +PairwiseMolecularInteraction.model_rebuild() +CellLineToEntityAssociationMixin.model_rebuild() +ChemicalEntityToEntityAssociationMixin.model_rebuild() +DrugToEntityAssociationMixin.model_rebuild() +ChemicalToEntityAssociationMixin.model_rebuild() +CaseToEntityAssociationMixin.model_rebuild() +ChemicalToChemicalAssociation.model_rebuild() +ReactionToParticipantAssociation.model_rebuild() +ReactionToCatalystAssociation.model_rebuild() +ChemicalToChemicalDerivationAssociation.model_rebuild() +MolecularActivityToPathwayAssociation.model_rebuild() +ChemicalToPathwayAssociation.model_rebuild() +NamedThingAssociatedWithLikelihoodOfNamedThingAssociation.model_rebuild() +ChemicalGeneInteractionAssociation.model_rebuild() +GeneRegulatesGeneAssociation.model_rebuild() +ProcessRegulatesProcessAssociation.model_rebuild() +ChemicalAffectsGeneAssociation.model_rebuild() +GeneAffectsChemicalAssociation.model_rebuild() +DrugToGeneAssociation.model_rebuild() +MaterialSampleToEntityAssociationMixin.model_rebuild() +MaterialSampleDerivationAssociation.model_rebuild() +DiseaseToEntityAssociationMixin.model_rebuild() +EntityToExposureEventAssociationMixin.model_rebuild() +DiseaseToExposureEventAssociation.model_rebuild() +EntityToOutcomeAssociationMixin.model_rebuild() +ExposureEventToOutcomeAssociation.model_rebuild() +FrequencyQualifierMixin.model_rebuild() +EntityToFeatureOrDiseaseQualifiersMixin.model_rebuild() +FeatureOrDiseaseQualifiersToEntityMixin.model_rebuild() +EntityToPhenotypicFeatureAssociationMixin.model_rebuild() +PhenotypicFeatureToEntityAssociationMixin.model_rebuild() +PhenotypicFeatureToPhenotypicFeatureAssociation.model_rebuild() +InformationContentEntityToNamedThingAssociation.model_rebuild() +EntityToDiseaseAssociationMixin.model_rebuild() +DiseaseOrPhenotypicFeatureToEntityAssociationMixin.model_rebuild() +DiseaseOrPhenotypicFeatureToLocationAssociation.model_rebuild() +DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation.model_rebuild() +EntityToDiseaseOrPhenotypicFeatureAssociationMixin.model_rebuild() +CellLineToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +ChemicalToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +MaterialSampleToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +GenotypeToEntityAssociationMixin.model_rebuild() +GenotypeToPhenotypicFeatureAssociation.model_rebuild() +ExposureEventToPhenotypicFeatureAssociation.model_rebuild() +DiseaseToPhenotypicFeatureAssociation.model_rebuild() +CaseToPhenotypicFeatureAssociation.model_rebuild() +BehaviorToBehavioralFeatureAssociation.model_rebuild() +GeneToEntityAssociationMixin.model_rebuild() +GeneToPathwayAssociation.model_rebuild() +VariantToEntityAssociationMixin.model_rebuild() +GeneToDiseaseOrPhenotypicFeatureAssociation.model_rebuild() +GeneToPhenotypicFeatureAssociation.model_rebuild() +GeneToDiseaseAssociation.model_rebuild() +CausalGeneToDiseaseAssociation.model_rebuild() +CorrelatedGeneToDiseaseAssociation.model_rebuild() +DruggableGeneToDiseaseAssociation.model_rebuild() +PhenotypicFeatureToDiseaseAssociation.model_rebuild() +VariantToGeneAssociation.model_rebuild() +VariantToGeneExpressionAssociation.model_rebuild() +VariantToPopulationAssociation.model_rebuild() +PopulationToPopulationAssociation.model_rebuild() +VariantToPhenotypicFeatureAssociation.model_rebuild() +VariantToDiseaseAssociation.model_rebuild() +GenotypeToDiseaseAssociation.model_rebuild() +ModelToDiseaseAssociationMixin.model_rebuild() +GeneAsAModelOfDiseaseAssociation.model_rebuild() +VariantAsAModelOfDiseaseAssociation.model_rebuild() +GenotypeAsAModelOfDiseaseAssociation.model_rebuild() +CellLineAsAModelOfDiseaseAssociation.model_rebuild() +OrganismalEntityAsAModelOfDiseaseAssociation.model_rebuild() +OrganismToOrganismAssociation.model_rebuild() +TaxonToTaxonAssociation.model_rebuild() +GeneHasVariantThatContributesToDiseaseAssociation.model_rebuild() +GeneToExpressionSiteAssociation.model_rebuild() +SequenceVariantModulatesTreatmentAssociation.model_rebuild() +FunctionalAssociation.model_rebuild() +MacromolecularMachineToEntityAssociationMixin.model_rebuild() +MacromolecularMachineToMolecularActivityAssociation.model_rebuild() +MacromolecularMachineToBiologicalProcessAssociation.model_rebuild() +MacromolecularMachineToCellularComponentAssociation.model_rebuild() +MolecularActivityToChemicalEntityAssociation.model_rebuild() +MolecularActivityToMolecularActivityAssociation.model_rebuild() +GeneToGoTermAssociation.model_rebuild() +EntityToDiseaseAssociation.model_rebuild() +EntityToPhenotypicFeatureAssociation.model_rebuild() +SequenceAssociation.model_rebuild() +GenomicSequenceLocalization.model_rebuild() +SequenceFeatureRelationship.model_rebuild() +TranscriptToGeneRelationship.model_rebuild() +GeneToGeneProductRelationship.model_rebuild() +ExonToTranscriptRelationship.model_rebuild() +ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation.model_rebuild() +AnatomicalEntityToAnatomicalEntityAssociation.model_rebuild() +AnatomicalEntityToAnatomicalEntityPartOfAssociation.model_rebuild() +AnatomicalEntityToAnatomicalEntityOntogenicAssociation.model_rebuild() +OrganismTaxonToEntityAssociation.model_rebuild() +OrganismTaxonToOrganismTaxonAssociation.model_rebuild() +OrganismTaxonToOrganismTaxonSpecialization.model_rebuild() +OrganismTaxonToOrganismTaxonInteraction.model_rebuild() +OrganismTaxonToEnvironmentAssociation.model_rebuild() diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml index 2e8f43205..2abfaaec7 100644 --- a/src/biolink_model/schema/biolink_model.yaml +++ b/src/biolink_model/schema/biolink_model.yaml @@ -6138,7 +6138,6 @@ slots: range: KnowledgeLevelEnum multivalued: false required: true - ifabsent: string(not_provided) examples: - value: knowledge_assertion - value: prediction @@ -6166,7 +6165,6 @@ slots: range: AgentTypeEnum multivalued: false required: true - ifabsent: string(not_provided) examples: - value: manual_agent - value: automated_agent diff --git a/src/biolink_model/scripts/classprefixes.py b/src/biolink_model/scripts/classprefixes.py index b25847fb2..1ca73160f 100644 --- a/src/biolink_model/scripts/classprefixes.py +++ b/src/biolink_model/scripts/classprefixes.py @@ -1,5 +1,5 @@ # Auto generated from class_prefixes.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-10-10T17:39:55 +# Generation date: 2024-10-10T16:31:01 # Schema: BiolinkClassPrefixes # # id: biolink-model-class-prefixes @@ -11,7 +11,7 @@ from jsonasobj2 import JsonObj, as_dict from typing import Optional, List, Union, Dict, ClassVar, Any from dataclasses import dataclass -from datetime import date, datetime +from datetime import date, datetime, time from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions from linkml_runtime.utils.slot import Slot @@ -50,7 +50,7 @@ -@dataclass +@dataclass(repr=False) class BiolinkClassPrefixMap(YAMLRoot): """ preferred order identifier prefixes per class in Biolink Model @@ -76,7 +76,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class BiolinkClassPrefixesCollection(YAMLRoot): """ collection of BiolinkClassPrefixes objects @@ -98,7 +98,7 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): super().__post_init__(**kwargs) -@dataclass +@dataclass(repr=False) class Prefix(YAMLRoot): _inherited_slots: ClassVar[List[str]] = []